About MBD4
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
MBD4 c.1395C>T, p.(Gly465=)
Classification
Benign
Variant description:
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is benign. Select a step to read what it means.
Benign.A benign classification under the recorded framework.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
LYFE Sciences is an AI system, and it can make mistakes.
Criteria may be applied incorrectly, sources may be misread, and a
confident-looking classification can still be wrong.
Double-check every criterion and its underlying evidence
before relying on any call.
01The reasoning
How it was classified
The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Pathogenic evidence criteria: 0
Benign evidence criteria: 5
Pathogenic criteria applied · 0
No pathogenic criterion marked as applied in the recorded assessment.
Benign criteria applied · 5
BA1Stand alone
BA1 · stand alone
This variant is present at extremely high frequency in gnomAD v2.1 (AF=11.619%, 32,849/282,718 alleles, 2,604 homozygotes) and gnomAD v4.1 (AF=11.034%, 178,028/1,613,452 alleles, 11,984 homozygotes). Highest subpopulation frequency in South Asian population (v2.1 AF=24.819%, v4.1 AF=24.583%, grpmax FAF=24.313%). Far exceeds the BA1 threshold of >1% allele frequency in any general population. This variant is a common polymorphism.
BS1Strong
BS1 · strong
Variant is present at allele frequencies far exceeding the expected frequency for any MBD4-related autosomal dominant disorder. gnomAD v2.1 AF=11.619% overall, with subpopulation frequencies ranging from 3.9% (Finnish) to 24.8% (South Asian). In every subpopulation, the frequency exceeds the BS1 threshold of >0.3%. The variant is observed in 2,604 homozygous individuals in v2.1 alone, incompatible with a highly penetrant Mendelian disease.
BS2Strong
BS2 · strong
The variant is observed in homozygous state in 2,604 individuals in gnomAD v2.1 and 11,984 individuals in gnomAD v4.1. For a gene where germline loss-of-function variants are associated with a multi-tumor predisposition syndrome (per PVS1 gene context), observation of this many homozygotes in population databases is incompatible with a pathogenic role. The homozygous count far exceeds what would be expected for a disease-causing variant.
BP4Supporting
BP4 · supporting
Multiple lines of computational evidence support no impact on splicing or gene product. SpliceAI predicts no splicing alteration (max delta score 0.02, below the 0.1 threshold). The variant is synonymous (p.Gly465=) and produces no amino acid change. No in silico tool predicts a damaging consequence.
BP7Supporting
BP7 · supporting
This is a synonymous variant (p.Gly465=) for which splice prediction algorithms predict no impact to the splice consensus sequence or creation of a new splice site (SpliceAI max delta score 0.02). The nucleotide at this position is not highly conserved, as evidenced by the extremely high population frequency (gnomAD AF 11.6%, 2,604 homozygotes), which is incompatible with a position under strong purifying selection.
Recorded classification: Benign
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BA1 stand-alone benign, BS1 strong benign, BS2 strong benign, BP4 supporting benign, BP7 supporting benign; combination = 1 stand-alone benign + 2 strong benign + 2 supporting benign, which maps to Benign.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
178,028 / 1,613,452 alleles
gnomAD v4.1: 178,028 / 1,613,452 alleles. Recorded AF 0.11034. Recorded homozygote count 11984.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.11619; MAF= 11.61900%, 32849/282718 alleles, homozygotes = 2604) and has highest observed frequency in the South Asian population (AF= 0.248187; MAF= 24.81871%, 7598/30614 alleles, homozygotes = 1009); grpmax FAF= 0.243522.
gnomAD-Canada
This variant is present in gnomAD-Canada v1.0 (AF= 0.12491853139257006, 2300/18412 alleles, homozygotes = 167).
SpliceAI score
0.020 maximum delta
Recorded SpliceAI maximum delta score: 0.020. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
5 reported laboratory submissions
5 Benign. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
Context only
ClinVar ↗
Functional evidence
Statement recorded
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
No listed criterion applied
OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
Context only
For specialists
Technical detail
ACMG/AMP criteria under Not recorded, with the data and sources behind each one.
26 criteria with recorded statuses: 5 met · 18 not met · 0 not assessed · 3 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_001276270.2:c.1395C>T (p.Gly465=) is a synonymous variant in MBD4 present at extremely high frequency in population databases.
In gnomAD v2.1, this variant is observed in 32,849 of 282,718 alleles (AF=11.619%) including 2,604 homozygotes, with the highest subpopulation frequency in South Asians (AF=24.819%, 1,009 homozygotes).
In gnomAD v4.1, this variant is observed in 178,028 of 1,613,452 alleles (AF=11.034%) including 11,984 homozygotes.
The allele frequency far exceeds the BA1 stand-alone benign threshold of >1% in any general population, establishing this variant as a common polymorphism.
SpliceAI predicts no splicing impact (max delta score 0.02), consistent with the synonymous nature of this substitution.
Five clinical laboratories in ClinVar have classified this variant as Benign (ClinVarID 1262431), though review status is single-submitter level without expert panel consensus.
No functional studies, segregation data, or de novo observations for this variant were identified in the reviewed literature.
The very high population frequency (11.6% overall, thousands of homozygotes) alone is sufficient to classify this variant as Benign under generic ACMG/AMP 2015 framework.
No criteria match.
Met · 5
BA1 Stand aloneThis variant is present at extremely high frequency in gnomAD v2.1 (AF=11.619%, 32,849/282,718 alleles, 2,604 homozygotes) and gnomAD v4.1 (AF=11.034%, 178,028/1,613,452 alleles, 11,984 homozygotes). Highest subpopulation frequency in South Asian population (v2.1 AF=24.819%, v4.1 AF=24.583%, grpmax FAF=24.313%). Far exceeds the BA1 threshold of >1% allele frequency in any general population. This variant is a common polymorphism. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1 overall AF 11.6% with 2
- 604 homozygotes
- SAS subpopulation AF 24.8% with 1
- 009 homozygotes
- gnomAD v4.1 overall AF 11.0% with 11
- 984 homozygotes
- SAS subpopulation AF 24.6% with 2
- 999 homozygotes
Sources
BS1 StrongVariant is present at allele frequencies far exceeding the expected frequency for any MBD4-related autosomal dominant disorder. gnomAD v2.1 AF=11.619% overall, with subpopulation frequencies ranging from 3.9% (Finnish) to 24.8% (South Asian). In every subpopulation, the frequency exceeds the BS1 threshold of >0.3%. The variant is observed in 2,604 homozygous individuals in v2.1 alone, incompatible with a highly penetrant Mendelian disease. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1 AF 11.6% (all populations >0.3%)
- 2
- 604 homozygotes
- v4.1 AF 11.0% with 11
- 984 homozygotes
Sources
BS2 StrongThe variant is observed in homozygous state in 2,604 individuals in gnomAD v2.1 and 11,984 individuals in gnomAD v4.1. For a gene where germline loss-of-function variants are associated with a multi-tumor predisposition syndrome (per PVS1 gene context), observation of this many homozygotes in population databases is incompatible with a pathogenic role. The homozygous count far exceeds what would be expected for a disease-causing variant. Details ▾Hide ▴
Evidence considered
- 2
- 604 homozygotes in gnomAD v2.1
- 11
- 984 homozygotes in gnomAD v4.1
- MBD4 LoF associated with multi-tumor predisposition syndrome
Sources
BP4 SupportingMultiple lines of computational evidence support no impact on splicing or gene product. SpliceAI predicts no splicing alteration (max delta score 0.02, below the 0.1 threshold). The variant is synonymous (p.Gly465=) and produces no amino acid change. No in silico tool predicts a damaging consequence. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.02 — no predicted splicing impact
- synonymous variant with preserved amino acid sequence
Sources
BP7 SupportingThis is a synonymous variant (p.Gly465=) for which splice prediction algorithms predict no impact to the splice consensus sequence or creation of a new splice site (SpliceAI max delta score 0.02). The nucleotide at this position is not highly conserved, as evidenced by the extremely high population frequency (gnomAD AF 11.6%, 2,604 homozygotes), which is incompatible with a position under strong purifying selection. Details ▾Hide ▴
Evidence considered
- Synonymous p.Gly465=
- SpliceAI max delta 0.02 — no predicted splice alteration
- nucleotide not conserved as shown by high gnomAD AF 11.6% with 2
- 604 homozygotes
Sources
Not met · 18 · evaluated, threshold not reached
PS1 Synonymous variant produces no amino acid change (p.Gly465=). PS1 requires the variant to result in the same amino acid change as a previously established pathogenic variant, which cannot be satisfied by a synonymous substitution. Details ▾Hide ▴
Evidence considered
- Synonymous substitution with no amino acid change
PS2 No de novo data identified for this variant. No publications or ClinVar submissions report confirmed de novo observation. Details ▾Hide ▴
Evidence considered
- No de novo reports in ClinVar submissions or literature
Still missing
- No de novo testing data available
Sources
PS3 No functional data identified for this variant. No publications report experimental characterization of NM_001276270.2:c.1395C>T or a systematically characterized range that includes this position. This is a synonymous variant with no predicted functional consequence. Details ▾Hide ▴
Evidence considered
- No variant-specific functional studies found in literature or OncoKB
Still missing
- No functional studies available for this synonymous variant
Sources
PS4 Extremely high population frequency (gnomAD AF 11.6%, 2,604 homozygotes) precludes case-control enrichment. A variant this common cannot demonstrate statistically significant enrichment in affected individuals, regardless of any case observations. Details ▾Hide ▴
Evidence considered
- gnomAD AF 11.6% with 2
- 604 homozygotes makes PS4 unattainable
Sources
PM1 Synonymous variant (p.Gly465=) produces no amino acid change and therefore does not alter or remove any protein domain. No critical functional domain is affected by this silent substitution. Cancerhotspots.org does not flag this position as a significant hotspot. Details ▾Hide ▴
Evidence considered
- Synonymous variant does not disrupt protein domains
- position not in cancer hotspot
Sources
pvs1_gene_context
PM2 Variant is present at very high frequency in gnomAD v2.1 (AF=11.619%, 32,849/282,718 alleles, 2,604 homozygotes) and v4.1 (AF=11.034%, 178,028/1,613,452 alleles, 11,984 homozygotes). PM2 requires absence or very low frequency (<0.1%), which is far exceeded. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1 AF 11.6%
- gnomAD v4.1 AF 11.0% — far above PM2 threshold of <0.1%
Sources
PM6 No confirmed de novo observation for this variant in any publication or ClinVar submission. Assumed de novo without confirmation of maternity/paternity does not satisfy PM6. Details ▾Hide ▴
Evidence considered
- No de novo reports identified
Still missing
- No de novo data available
Sources
PP1 No segregation data available for this variant. No family studies or co-segregation analyses identified in the literature or ClinVar submissions. Details ▾Hide ▴
Evidence considered
- No segregation or family data identified
Still missing
- No segregation analysis available
Sources
PP2 PP2 applies to missense variants in genes with low rate of benign missense variation and where missense is a common pathogenic mechanism. This variant is synonymous, not missense, and MBD4 has a loss-of-function mechanism with supporting truncating variants per PVS1 gene context. Details ▾Hide ▴
Evidence considered
- Synonymous variant
- PP2 is specific to missense variants
Sources
pvs1_gene_context
PP3 Multiple lines of in silico evidence predict no deleterious effect. SpliceAI predicts no splicing impact (max delta score 0.02). REVEL and BayesDel scores are not available. No evidence supports a damaging prediction for this synonymous variant. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.02 — no splicing impact predicted
- synonymous variant with no predicted protein effect
Sources
PP4 No patient phenotype data specific to this variant available. The variant is too common (AF 11.6%) to be specifically associated with any rare disease phenotype. Details ▾Hide ▴
Evidence considered
- No specific phenotype data
- high population frequency inconsistent with rare disease association
Still missing
- No patient phenotype information available
Sources
PP5 ClinVar classification is Benign (ClinVarID 1262431) with review status 'criteria provided, single submitter' (1-star). PP5 requires 3-star expert panel review status to apply at supporting strength per current framework. ClinVar submission audit shows 5 clinical laboratories classified as Benign, but no expert panel review. Details ▾Hide ▴
Evidence considered
- ClinVar Benign (5 labs)
- review status 'criteria provided
- single submitter' — insufficient star rating for PP5 application
Still missing
- No 3-star expert panel review in ClinVar
Sources
BS3 No experimental functional studies demonstrating no deleterious effect were identified in the literature or OncoKB. While the synonymous nature and absence of splicing impact (SpliceAI max delta 0.02) are consistent with a benign effect, BS3 requires direct experimental evidence such as enzymatic assays or model organism studies showing no functional impact. Details ▾Hide ▴
Evidence considered
- No direct experimental functional studies demonstrating benign effect identified
- in silico predictions alone insufficient for BS3
Still missing
- No experimental functional studies demonstrating no deleterious effect
Sources
BS4 No segregation data demonstrating lack of segregation with disease is available. No family studies involving this variant were identified. Details ▾Hide ▴
Evidence considered
- No family segregation data available
Still missing
- No segregation data for this variant
BP2 No evidence of this variant observed in trans with a pathogenic variant for a fully penetrant dominant disorder. While the variant is observed in homozygous state (2,604 homozygotes in gnomAD v2.1), the presence of homozygotes in a dominant disorder gene is better captured by BS2 and BA1 rather than BP2 (which requires specific trans configuration evidence). Details ▾Hide ▴
Evidence considered
- No trans-configuration data with pathogenic variant available
Still missing
- No trans configuration data
BP5 No evidence of an alternative molecular basis for disease in a patient carrying this variant. No case-level data with alternative molecular diagnoses is available. Details ▾Hide ▴
Evidence considered
- No alternative molecular cause identified in patients carrying this variant
Still missing
- No case-level data with alternative diagnoses
BP6 ClinVar classification is Benign with review status 'criteria provided, single submitter' (1-star). BP6 requires 3-star expert panel review status to apply at supporting benign strength. Although 5 clinical laboratories submitted Benign classifications, the absence of expert panel consensus precludes BP6 application. Details ▾Hide ▴
Evidence considered
- ClinVar Benign
- 5 clinical laboratories
- review status 'criteria provided
- single submitter' — 1-star
- insufficient for BP6
Still missing
- No 3-star expert panel review in ClinVar
Sources
PS5 No evidence for PS5 (alternate pathogenic variant at same position in ClinVar) identified. The variant is synonymous; no alternate missense variant at the same residue exists to satisfy this criterion. Details ▾Hide ▴
Evidence considered
- Synonymous variant with no ClinVar alternate pathogenic missense at same codon
Sources
clinvar ↗pm5_candidates
Not applicable · 3· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ASynonymous variant (p.Gly465=) does not trigger PVS1 null-variant framework. Variant bucket classified as 'other' in PVS1 variant assessment; no nonsense, frameshift, or canonical splice consensus disruption. Details ▾Hide ▴
Evidence considered
- Synonymous substitution with no predicted protein truncation or splice-site disruption
Sources
pvs1_variant_assessment
PM5 N/ASynonymous variant (p.Gly465=) — no amino acid change, no residue to compare against alternate pathogenic missense variants. PM5 candidate assessment confirms: unable to parse missense residue context. Details ▾Hide ▴
Evidence considered
- Synonymous substitution with no amino acid change
- no same-residue comparator possible
Sources
pm5_candidates
BP1 N/ABP1 applies specifically to missense variants in genes where primarily truncating variants cause disease. This variant is synonymous (p.Gly465=), not missense. The criterion does not apply. Details ▾Hide ▴
Evidence considered
- Synonymous variant
- not missense
- BP1 missense-specific criterion does not apply
Sources
pvs1_gene_context
Identifiers
- Gene
- MBD4
- Transcript
- NM_001276270.2
- Coding (HGVS c.)
- NM_001276270.2:c.1395C>T
- Protein (HGVS p.)
- NP_001263199.1:p.(Gly465=)
- GRCh38
- chr3:129433246 G>A
- GRCh37
- chr3:129152089 G>A
- ClinVar
- 1262431
Gene diagram
Every interpreted variant in MBD4, mapped onto the exon structure of NM_001276270.2. Select a row to find it on the plot.
MBD4NM_001276270.2
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in MBD4
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Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
178,028 / 1,613,452 alleles
AF 0.11 · 11984 homozygotes · FAF 0.243
gnomAD v2.1
32,849 / 282,718 alleles
AF 0.116 · 2604 homozygotes · FAF 0.244
gnomAD-Canada v1.0
Allele count data not recorded
By genetic ancestry
gnomAD v4.1
AF 0.11 · 178028 / 1,613,452 alleles · 11984 hom · FAF 0.24
| South Asian22384 / 91,056 | 0.252999 hom |
| African/African American16543 / 74,950 | 0.221864 hom |
| Ashkenazi Jewish4957 / 29,598 | 0.17426 hom |
| Middle Eastern947 / 6,062 | 0.1694 hom |
| Remaining individuals7640 / 62,488 | 0.12533 hom |
| Amish96 / 912 | 0.115 hom |
| European (non-Finnish)114917 / 1,179,522 | 0.0975619 hom |
| Admixed American4913 / 60,018 | 0.082245 hom |
| East Asian2983 / 44,876 | 0.066130 hom |
| European (Finnish)2648 / 63,970 | 0.04169 hom |
gnomAD v2.1
AF 0.12 · 32849 / 282,718 alleles · 2604 hom · FAF 0.24
| South Asian7598 / 30,614 | 0.251009 hom |
| African/African American5425 / 24,936 | 0.22606 hom |
| Ashkenazi Jewish1729 / 10,370 | 0.17139 hom |
| Remaining individuals848 / 7,212 | 0.1259 hom |
| European (non-Finnish)12250 / 129,112 | 0.095592 hom |
| East Asian1527 / 19,946 | 0.07766 hom |
| Admixed American2485 / 35,436 | 0.07110 hom |
| European (Finnish)987 / 25,092 | 0.03923 hom |
gnomAD-Canada
AF not recorded · ? / ? alleles
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 0.11034; MAF= 11.03398%, 178028/1613452 alleles, homozygotes = 11984) and has highest observed frequency in the South Asian population (AF= 0.245827; MAF= 24.58267%, 22384/91056 alleles, homozygotes = 2999); grpmax FAF= 0.24313.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.11619; MAF= 11.61900%, 32849/282718 alleles, homozygotes = 2604) and has highest observed frequency in the South Asian population (AF= 0.248187; MAF= 24.81871%, 7598/30614 alleles, homozygotes = 1009); grpmax FAF= 0.243522.
gnomAD-Canada
This variant is present in gnomAD-Canada v1.0 (AF= 0.12491853139257006, 2300/18412 alleles, homozygotes = 167).
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
BP4 SupportingMultiple lines of computational evidence support no impact on splicing or gene product. SpliceAI predicts no splicing alteration (max delta score 0.02, below the 0.1 threshold). The variant is synonymous (p.Gly465=) and produces no amino acid change. No in silico tool predicts a damaging consequence. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.02 — no predicted splicing impact
- synonymous variant with preserved amino acid sequence
Sources
BP7 SupportingThis is a synonymous variant (p.Gly465=) for which splice prediction algorithms predict no impact to the splice consensus sequence or creation of a new splice site (SpliceAI max delta score 0.02). The nucleotide at this position is not highly conserved, as evidenced by the extremely high population frequency (gnomAD AF 11.6%, 2,604 homozygotes), which is incompatible with a position under strong purifying selection. Details ▾Hide ▴
Evidence considered
- Synonymous p.Gly465=
- SpliceAI max delta 0.02 — no predicted splice alteration
- nucleotide not conserved as shown by high gnomAD AF 11.6% with 2
- 604 homozygotes
Sources
PP3 Multiple lines of in silico evidence predict no deleterious effect. SpliceAI predicts no splicing impact (max delta score 0.02). REVEL and BayesDel scores are not available. No evidence supports a damaging prediction for this synonymous variant. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.02 — no splicing impact predicted
- synonymous variant with no predicted protein effect
Sources
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
7 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Recorded publications
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PMID 23619275 ↗ACMG position statement on prenatal/preconception expanded carrier screening.ACMG position statement on prenatal/preconception expanded carrier screening. Discusses criteria for selecting disorders for carrier screening panels. NM_001276270.2:c.1395C>T was not identified in this paper.Does not name this variant
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PMID 25730230 ↗Expanded carrier screening in reproductive medicine-points to consider: a joint statement of the American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, National Society of Genetic Counselors, Perinatal Quality Foundation, and Society for Maternal-Fetal Medicine.Edwards JG et al. · 2015Joint statement on expanded carrier screening in reproductive medicine from ACMG, ACOG, NSGC, Perinatal Quality Foundation, and SMFM. Provides points to consider for expanded carrier screening panels. NM_001276270.2:c.1395C>T was not identified in this paper.Does not name this variant
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PMID 25741868 ↗Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.ACMG/AMP 2015 guidelines for interpretation of sequence variants. This is a framework document describing variant classification standards and criteria. NM_001276270.2:c.1395C>T was not identified in this paper.Does not name this variant
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PMID 23169492 ↗The perspective from EASAC and FEAM on direct-to-consumer genetic testing for health-related purposes.Fears R et al. · 2013EASAC and FEAM perspective on direct-to-consumer genetic testing for health-related purposes. Discusses regulatory and ethical considerations of DTC genetic testing. NM_001276270.2:c.1395C>T was not identified in this paper.Does not name this variant
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PMID 22947299 ↗Specific guidelines for assessing and improving the methodological quality of economic evaluations of newborn screening.Langer A et al. · 2012Guidelines for assessing methodological quality of economic evaluations of newborn screening. NM_001276270.2:c.1395C>T was not identified in this paper.Does not name this variant
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PMID 23037933 ↗Including the initial newborn screening bloodspot collection device serial number on birth certificates: basis and recommendations from the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children.Therrell BL et al. · 2013Recommendations on including newborn screening bloodspot collection device serial numbers on birth certificates. NM_001276270.2:c.1395C>T was not identified in this paper.Does not name this variant
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PMID 28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Describes a systematic framework for variant classification. NM_001276270.2:c.1395C>T was not identified in this paper.Does not name this variant
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
178,028 / 1,613,452 recorded alleles
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.020
Open source ↗
ClinVar
5 Benign
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
Cancer hotspots
Captured Cancer Hotspots source record
Open source ↗
OncoKB
Captured OncoKB source record
Open source ↗
All source links
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/1262431/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/3-129152089-G-A?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr3-129433246-G-A?dataset=gn…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/3-129433246-G-A
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_001276270.2%3Ac.1…
- OncoKB ↗www.oncokb.org/gene/MBD4/G465=
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=MBD4+c.1395C%3ET
- Cancer hotspots ↗www.cancerhotspots.org/
Statements for reports
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 0.11034; MAF= 11.03398%, 178028/1613452 alleles, homozygotes = 11984) and has highest observed frequency in the South Asian population (AF= 0.245827; MAF= 24.58267%, 22384/91056 alleles, homozygotes = 2999); grpmax FAF= 0.24313.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.11619; MAF= 11.61900%, 32849/282718 alleles, homozygotes = 2604) and has highest observed frequency in the South Asian population (AF= 0.248187; MAF= 24.81871%, 7598/30614 alleles, homozygotes = 1009); grpmax FAF= 0.243522.
gnomAD-Canada
This variant is present in gnomAD-Canada v1.0 (AF= 0.12491853139257006, 2300/18412 alleles, homozygotes = 167).
ClinVar
This variant has been reported in ClinVar as Benign (5 clinical laboratories). (ClinVarID = 1262431)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
Functional
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
Somatic
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.