About SMARCA4
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
SMARCA4 c.3894C>T, p.(Asp1298=)
Classification
Likely benign
Variant description:
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is likely benign. Select a step to read what it means.
Likely benign.A likely 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: 3
Pathogenic criteria applied · 0
No pathogenic criterion marked as applied in the recorded assessment.
Benign criteria applied · 3
BP4Supporting
BP4 · supporting
Multiple lines of computational evidence support a benign interpretation. SpliceAI predicts no significant splice impact (max delta score 0.03). The variant is synonymous (p.Asp1298=) with no predicted effect on the primary amino acid sequence. The absence of REVEL and BayesDel scores is consistent with the synonymous nature of the variant and the inability of missense-focused tools to assess non-coding consequences.
BP6Supporting
BP6 · supporting
This variant has been classified as Likely benign by six clinical laboratories in ClinVar (ClinVar Variation ID: 238439). While the review status is 'criteria provided, single submitter' and no expert panel review has been performed, the consistent classification across multiple independent clinical laboratories supports a benign interpretation under BP6.
BP7Supporting
BP7 · supporting
BP7 is met: this is a synonymous variant (p.Asp1298=) at a nucleotide position where SpliceAI predicts no significant splice impact (max delta score 0.03, well below 0.1), and the nucleotide is not in a highly conserved splice consensus region. The variant falls in exon 28 (c.3874–3951) of the SMARCA4 transcript NM_001128849.3, distant from exon-intron boundaries.
Recorded classification: Likely 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: BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; combination = 3 supporting benign, which maps to Likely 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
60 / 1,613,590 alleles
gnomAD v4.1: 60 / 1,613,590 alleles. Recorded AF 3.71842e-05. Recorded homozygote count 0.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 4.77928e-05; MAF= 0.00478%, 12/251084 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000108767; MAF= 0.01088%, 2/18388 alleles, homozygotes = 0); grpmax FAF= 4.747e-05.
gnomAD-Canada
This variant is present in gnomAD-Canada v1.0 (AF= 0.0004887585532746823, 9/18414 alleles, homozygotes = 0).
No listed criterion applied
SpliceAI score
0.030 maximum delta
Recorded SpliceAI maximum delta score: 0.030. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
6 reported laboratory submissions
6 Likely benign.
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.
27 criteria with recorded statuses: 3 met · 17 not met · 0 not assessed · 7 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_001128849.3:c.3894C>T is a synonymous variant (p.Asp1298=) in the SMARCA4 gene. Synonymous variants that do not alter splicing are typically benign.
This variant is present in population databases at very low frequencies: gnomAD v2.1 (12/251,084 alleles, AF=0.0048%), gnomAD v4.1 (60/1,613,590 alleles, AF=0.0037%), and gnomAD-Canada (9/18,414 alleles, AF=0.049%). Population frequency alone is insufficient to classify this variant as benign or pathogenic by allele frequency thresholds.
SpliceAI predicts no significant impact on splicing (max delta score 0.03), and the synonymous nucleotide substitution is not predicted to create or disrupt a splice site. This supports a benign interpretation under both BP4 and BP7.
This variant has been reported in ClinVar as Likely benign by six clinical laboratories (ClinVar Variation ID: 238439). No laboratory has submitted a conflicting classification, supporting BP6.
No published literature was identified that specifically describes NM_001128849.3:c.3894C>T. All PMIDs associated with ClinVar submissions refer to methodological or guideline publications that do not mention this variant.
Applying generic ACMG/AMP 2015 combination rules (Richards et al., PMID:25741868): three supporting benign criteria are met (BP4, BP6, BP7) with no pathogenic criteria met. The combination of two or more supporting benign criteria is sufficient for a classification of Likely Benign.
No criteria match.
Met · 3
BP4 SupportingMultiple lines of computational evidence support a benign interpretation. SpliceAI predicts no significant splice impact (max delta score 0.03). The variant is synonymous (p.Asp1298=) with no predicted effect on the primary amino acid sequence. The absence of REVEL and BayesDel scores is consistent with the synonymous nature of the variant and the inability of missense-focused tools to assess non-coding consequences. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.03 (no splicing impact
- well below 0.1 threshold)
- Variant is synonymous with no predicted change to protein sequence
- Conservation-based and ensemble predictors (REVEL
- BayesDel) not applicable to synonymous change
Sources
BP6 SupportingThis variant has been classified as Likely benign by six clinical laboratories in ClinVar (ClinVar Variation ID: 238439). While the review status is 'criteria provided, single submitter' and no expert panel review has been performed, the consistent classification across multiple independent clinical laboratories supports a benign interpretation under BP6. Details ▾Hide ▴
Evidence considered
- ClinVar classification: Likely benign (6 clinical laboratories)
- Submitters include: Ambry Genetics
- Labcorp Genetics (Invitae)
- University of Chicago
- Sinai Health System
- Quest Diagnostics
- CeGaT
- No conflicting classifications submitted
Sources
BP7 SupportingBP7 is met: this is a synonymous variant (p.Asp1298=) at a nucleotide position where SpliceAI predicts no significant splice impact (max delta score 0.03, well below 0.1), and the nucleotide is not in a highly conserved splice consensus region. The variant falls in exon 28 (c.3874–3951) of the SMARCA4 transcript NM_001128849.3, distant from exon-intron boundaries. Details ▾Hide ▴
Evidence considered
- Synonymous variant: c.3894C>T
- p.Asp1298=
- SpliceAI max delta score = 0.03 (no splice site creation or disruption)
- Variant is internal to exon 28 (cds range c.3874–3951)
- not at splice consensus
- Nucleotide not in highly conserved splice region
Sources
Not met · 17 · evaluated, threshold not reached
PS2 No de novo observation data are available for this variant. PS2 requires confirmation of de novo occurrence with both maternity and paternity confirmed. Details ▾Hide ▴
Evidence considered
- No de novo reports identified in ClinVar submissions or published literature
Still missing
- No parental testing data available
PS3 No well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product have been identified for this variant. Details ▾Hide ▴
Evidence considered
- No functional study data identified for NM_001128849.3:c.3894C>T
- OncoKB classification is 'Unknown Oncogenic Effect' with no variant-specific functional evidence
Still missing
- No variant-specific functional studies available
PS4 No case-control data or sufficient statistical evidence demonstrates significantly higher prevalence of this variant in affected individuals compared to controls. Details ▾Hide ▴
Evidence considered
- No case-control studies or cohort data identified for this variant
- Variant is present in gnomAD population databases at very low frequency but no affected-vs-control comparison data available
Still missing
- No case-control or cohort prevalence data available
PM1 This variant does not reside in a known mutational hotspot or critical functional domain with statistically significant enrichment of pathogenic variation. Hotspot analysis confirms no residue-level significance, and OncoKB lists no established oncogenic hotspots at this position. Details ▾Hide ▴
Evidence considered
- Hotspot analysis: residue_significant=false
- exact_variant_listed='no'
- No statistically significant enrichment of pathogenic variants at codon 1298
Sources
PM2 This variant is present in multiple population databases (gnomAD v2.1: 12 alleles; v4.1: 60 alleles; gnomAD-Canada: 9 alleles) and is therefore not absent from controls. While the allele frequency is very low (~0.0048% overall), PM2 requires absence from population databases for dominant disorders. The variant is observed across diverse populations and datasets, inconsistent with the absence criterion. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: 12/251
- 084 alleles
- AF=4.78e-05
- 0 homozygotes
- gnomAD v4.1: 60/1
- 613
- 590 alleles
- AF=3.72e-05
- gnomAD-Canada: 9/18
- 414 alleles
- AF=4.89e-04
- Variant is present (not absent) across multiple population databases
Sources
PM6 No assumed de novo observation data are available. PM6 requires the variant to be assumed de novo with maternity and paternity not confirmed. No de novo context was reported in ClinVar submissions or the literature reviewed. Details ▾Hide ▴
Evidence considered
- No de novo reports in ClinVar submissions
- No de novo context identified in literature
Still missing
- No de novo data available
PP1 No cosegregation data are available for this variant. PP1 requires demonstration of cosegregation with disease in multiple affected family members. Details ▾Hide ▴
Evidence considered
- No family studies or cosegregation data identified
Still missing
- No segregation analysis data available
PP3 No in silico predictors support a pathogenic effect. SpliceAI shows a maximum delta score of 0.03, well below the threshold for splice-altering prediction. REVEL and BayesDel scores are not available for this synonymous variant, which is expected as these tools are designed for missense substitutions. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta score = 0.03 (no significant splice impact predicted)
- REVEL not available (synonymous variant
- no amino acid change)
- BayesDel not available (synonymous variant
Sources
PP4 No patient phenotype data specific to this variant are available. PP4 requires that the patient's phenotype or family history is highly specific for a disease with a single genetic etiology. Details ▾Hide ▴
Evidence considered
- No phenotype data for probands carrying this variant identified
Still missing
- No patient phenotype data available
PP5 PP5 is not met: ClinVar reports this variant as Likely benign, not pathogenic. PP5 requires a reputable source to have recently reported the variant as pathogenic. The six clinical laboratory submissions in ClinVar unanimously classify this variant as Likely benign. Details ▾Hide ▴
Evidence considered
- ClinVar classification: Likely benign (6 clinical laboratories)
- Review status: criteria provided
- single submitter
- No reputable source reports this variant as pathogenic
Sources
BA1 BA1 is not met: the maximum allele frequency across population databases is approximately 0.0048% (gnomAD v2.1) to 0.049% (gnomAD-Canada), well below the 1% threshold required for BA1. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1 AF = 4.78e-05 (0.0048%)
- gnomAD v4.1 AF = 3.72e-05 (0.0037%)
- gnomAD-Canada AF = 4.89e-04 (0.049%)
- All frequencies well below 1% threshold
Sources
BS1 BS1 is not met: while the variant is observed in population databases, the maximum allele frequency (0.049% in gnomAD-Canada) remains below the 0.3% threshold required for BS1. Details ▾Hide ▴
Evidence considered
- Max observed AF = 4.89e-04 (0.049%) in gnomAD-Canada
- Below 0.3% threshold required for BS1
Sources
BS2 No data are available regarding observation of this variant in a healthy adult individual in trans with a dominant disorder, or in a homozygous state for a recessive disorder with no phenotype. No homozygous observations are reported in gnomAD. Details ▾Hide ▴
Evidence considered
- No homozygotes observed in any gnomAD dataset
- No trans-phase or genotype-phenotype data available
Still missing
- No individual-level genotype-phenotype correlation data available
BS3 No well-established in vitro or in vivo functional studies demonstrating no damaging effect on protein function or splicing have been identified for this variant. Details ▾Hide ▴
Evidence considered
- No functional studies evaluating this specific variant identified
Still missing
- No variant-specific functional studies available
BS4 No segregation or family data are available to assess lack of cosegregation with disease. BS4 requires demonstration that the variant does not segregate with disease in affected family members. Details ▾Hide ▴
Evidence considered
- No family studies or cosegregation data identified
Still missing
- No segregation analysis data available
BP2 No data are available regarding observation of this variant in trans with a known pathogenic variant, or in cis with a pathogenic variant, in any individual. Details ▾Hide ▴
Evidence considered
- No co-occurrence or phase data identified
Still missing
- No phase or co-occurrence data available
BP5 No data are available demonstrating that this variant has been observed in a case with an alternative molecular basis for disease. BP5 requires identification of an alternate causal variant in a case where this variant is also present. Details ▾Hide ▴
Evidence considered
- No case-level data with alternative molecular findings identified
Still missing
- No case-level genetic data available
Not applicable · 7· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/APVS1 is not applicable: NM_001128849.3:c.3894C>T is a synonymous variant (p.Asp1298=) and does not fall into any null-variant bucket (nonsense, frameshift, or canonical ±1,2 splice consensus). Variant-specific PVS1 assessment confirms apply_generic_pvs1_framework=false, variant_bucket=other. Details ▾Hide ▴
Evidence considered
- Variant resolved to synonymous change NP_001122321.1:p.(Asp1298=)
- PVS1 variant assessment: variant_bucket=other
- apply_generic_pvs1_framework=false
- Synonymous variants do not trigger loss-of-function mechanism required for PVS1
Sources
pvs1_generic_framework ↗pvs1_variant_assessment
PS1 N/APS1 is not applicable: this is a synonymous variant with no amino acid change. PS1 requires a nucleotide change producing the same amino acid change as a previously established pathogenic missense variant. Details ▾Hide ▴
Evidence considered
- Synonymous variant p.Asp1298= produces no amino acid change
- No established pathogenic variant with same amino acid change is applicable
PM5 N/APM5 is not applicable: this variant resolves to a synonymous change (p.Asp1298=) rather than a missense alteration. PM5 requires a novel missense change at the same amino acid residue as another pathogenic missense variant. The PM5 candidate analysis confirms inability to parse missense residue context from the normalized protein consequence. Details ▾Hide ▴
Evidence considered
- Protein consequence is synonymous: NP_001122321.1:p.(Asp1298=)
- PM5 candidate analysis: 'Unable to parse missense residue context from normalized protein consequence'
Sources
pm5_candidates
PP2 N/APP2 is not applicable: this is a synonymous variant, not a missense change. PP2 applies specifically to missense variants in genes where missense variation is a common mechanism of disease and benign missense variation is rare. Details ▾Hide ▴
Evidence considered
- Variant is synonymous (p.Asp1298=)
- not missense
BP1 N/ABP1 is not applicable: this is a synonymous variant, not a missense change. BP1 applies specifically to missense variants in genes where truncating variants are the primary known mechanism of disease. Details ▾Hide ▴
Evidence considered
- Variant is synonymous (p.Asp1298=)
- not missense
BP3 N/ASkipped per task specification: BP3 applies to in-frame deletions/insertions in repetitive regions, which is not relevant to this single-nucleotide synonymous substitution. Details ▾Hide ▴
No further detail was recorded.
PS5 N/APS5 is not applicable: this is a synonymous variant with no amino acid change. PS5 applies only to novel missense variants at an amino acid residue where a different missense change has been established as pathogenic. Details ▾Hide ▴
Evidence considered
- Synonymous variant p.Asp1298= involves no amino acid change
Identifiers
- Gene
- SMARCA4
- Transcript
- NM_001128849.3
- Coding (HGVS c.)
- NM_001128849.3:c.3894C>T
- Protein (HGVS p.)
- NP_001122321.1:p.(Asp1298=)
- GRCh38
- chr19:11034143 C>T
- GRCh37
- chr19:11144819 C>T
- ClinVar
- 470376, 238439
Gene diagram
Every interpreted variant in SMARCA4, mapped onto the exon structure of NM_001128849.3. Select a row to find it on the plot.
SMARCA4NM_001128849.3
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 SMARCA4
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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
60 / 1,613,590 alleles
AF 3.72e-05 · 0 homozygotes · FAF 3.78e-05
gnomAD v2.1
12 / 251,084 alleles
AF 4.78e-05 · 0 homozygotes · FAF 4.75e-05
gnomAD-Canada v1.0
Allele count data not recorded
By genetic ancestry
gnomAD v4.1
AF 3.7e-05 · 60 / 1,613,590 alleles · 0 hom · FAF 3.8e-05
| European (non-Finnish)57 / 1,179,900 | 4.8e-05 |
| East Asian2 / 44,900 | 4.5e-05 |
| Remaining individuals1 / 62,484 | 1.6e-05 |
0 alternate alleles recorded in 7 other groups: Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.
gnomAD v2.1
AF 4.8e-05 · 12 / 251,084 alleles · 0 hom · FAF 4.7e-05
| East Asian2 / 18,388 | 0.00011 |
| European (non-Finnish)10 / 113,440 | 8.8e-05 |
0 alternate alleles recorded in 6 other groups: African/African American, Admixed American, Ashkenazi Jewish, European (Finnish), Remaining individuals, South Asian.
gnomAD-Canada
AF not recorded · ? / ? alleles
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 3.71842e-05; MAF= 0.00372%, 60/1613590 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 4.83092e-05; MAF= 0.00483%, 57/1179900 alleles, homozygotes = 0); grpmax FAF= 3.775e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 4.77928e-05; MAF= 0.00478%, 12/251084 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000108767; MAF= 0.01088%, 2/18388 alleles, homozygotes = 0); grpmax FAF= 4.747e-05.
gnomAD-Canada
This variant is present in gnomAD-Canada v1.0 (AF= 0.0004887585532746823, 9/18414 alleles, homozygotes = 0).
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
BP4 SupportingMultiple lines of computational evidence support a benign interpretation. SpliceAI predicts no significant splice impact (max delta score 0.03). The variant is synonymous (p.Asp1298=) with no predicted effect on the primary amino acid sequence. The absence of REVEL and BayesDel scores is consistent with the synonymous nature of the variant and the inability of missense-focused tools to assess non-coding consequences. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.03 (no splicing impact
- well below 0.1 threshold)
- Variant is synonymous with no predicted change to protein sequence
- Conservation-based and ensemble predictors (REVEL
- BayesDel) not applicable to synonymous change
Sources
BP7 SupportingBP7 is met: this is a synonymous variant (p.Asp1298=) at a nucleotide position where SpliceAI predicts no significant splice impact (max delta score 0.03, well below 0.1), and the nucleotide is not in a highly conserved splice consensus region. The variant falls in exon 28 (c.3874–3951) of the SMARCA4 transcript NM_001128849.3, distant from exon-intron boundaries. Details ▾Hide ▴
Evidence considered
- Synonymous variant: c.3894C>T
- p.Asp1298=
- SpliceAI max delta score = 0.03 (no splice site creation or disruption)
- Variant is internal to exon 28 (cds range c.3874–3951)
- not at splice consensus
- Nucleotide not in highly conserved splice region
Sources
PP3 No in silico predictors support a pathogenic effect. SpliceAI shows a maximum delta score of 0.03, well below the threshold for splice-altering prediction. REVEL and BayesDel scores are not available for this synonymous variant, which is expected as these tools are designed for missense substitutions. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta score = 0.03 (no significant splice impact predicted)
- REVEL not available (synonymous variant
- no amino acid change)
- BayesDel not available (synonymous variant
Sources
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03).
5 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
-
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.Richards S et al. · 2015Standards and guidelines for the interpretation of sequence variants. This is the foundational ACMG/AMP 2015 framework paper describing variant classification criteria and combination rules. NM_001128849.3:c.3894C>T is not discussed.Does not name this variant
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PMID 26467025 ↗A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.Karbassi I et al. · 2016A standardized DNA variant scoring system for pathogenicity assessments in Mendelian disorders (Karbassi et al., 2016). Describes a quantitative rules-based scoring framework applied to 11,894 variants across 338 genes. NM_001128849.3:c.3894C>T is not specifically discussed.Does not name this variant
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PMID 25394175 ↗A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment.Hampel H et al. · 2015ACMG and NSGC practice guideline for cancer predisposition referral indications (Hampel et al., 2015). Provides referral criteria for hereditary cancer syndromes. SMARCA4 is mentioned among cancer predisposition genes, but the specific variant c.3894C>T is not discussed.Does not name this variant
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PMID 29215836 ↗Rhabdoid Tumor Predisposition Syndrome.Adam MP et al. · 1993Rhabdoid Tumor Predisposition Syndrome GeneReviews entry (Adam et al.). Provides clinical overview of RTPS2 caused by germline SMARCA4 pathogenic variants. NM_001128849.3:c.3894C>T is not specifically discussed.Does not name this variant
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PMID 28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.Nykamp K et al. · 2017Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria (Nykamp et al., 2017). Describes a refined evidence-based classification system. NM_001128849.3:c.3894C>T is not discussed.Does not name this variant
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
60 / 1,613,590 recorded alleles
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.030
Open source ↗
ClinVar
6 Likely 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/238439/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/19-11144819-C-T?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr19-11034143-C-T?dataset=gn…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/19-11034143-C-T
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_001128849.3%3Ac.3…
- OncoKB ↗www.oncokb.org/gene/SMARCA4/D1298=
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=SMARCA4+c.3894C%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= 3.71842e-05; MAF= 0.00372%, 60/1613590 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 4.83092e-05; MAF= 0.00483%, 57/1179900 alleles, homozygotes = 0); grpmax FAF= 3.775e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 4.77928e-05; MAF= 0.00478%, 12/251084 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000108767; MAF= 0.01088%, 2/18388 alleles, homozygotes = 0); grpmax FAF= 4.747e-05.
gnomAD-Canada
This variant is present in gnomAD-Canada v1.0 (AF= 0.0004887585532746823, 9/18414 alleles, homozygotes = 0).
ClinVar
This variant has been reported in ClinVar as Likely benign (6 clinical laboratories). (ClinVarID = 238439)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03).
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.