About PTEN
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
PTEN c.165-7T>C, p.?
Classification
Uncertain significance
Variant description:
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
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 ClinGen PTEN VCEP v3.2.0. 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: 1
Pathogenic criteria applied · 0
No pathogenic criterion marked as applied in the recorded assessment.
Benign criteria applied · 1
BS1Strong
BS1 · strong
PTEN VCEP v3.2.0 BS1_Strong applies when gnomAD filtering allele frequency is between 0.0043% (0.000043) and 0.056% (0.00056). The gnomAD v4.1 grpmax filtering allele frequency for this variant is 5.997e-05 (0.006%), which falls within the BS1_Strong range. This indicates the variant is observed at a population frequency greater than expected for a highly penetrant autosomal dominant disorder like PTEN hamartoma tumor syndrome.
Recorded classification: Uncertain significance
Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework was evaluated deterministically with applied criteria: BS1 strong benign; no rule matched the adjudicated criteria.
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
11 / 1,587,106 alleles
gnomAD v4.1: 11 / 1,587,106 alleles. Recorded AF 6.93085e-06. Recorded homozygote count 0.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 4.2304e-06; MAF= 0.00042%, 1/236384 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.34986e-05; MAF= 0.00335%, 1/29852 alleles, homozygotes = 0).
SpliceAI score
0.020 maximum delta
Recorded SpliceAI maximum delta score: 0.020. Refer to the recorded PP3/BP4 rationale for interpretation.
No listed criterion applied
SpliceAI ↗
ClinVar submissions
5 reported laboratory submissions
5 Likely benign.
Context only
ClinVar ↗
No screenshot for this evidence
Functional evidence
Not recorded
No standalone functional evidence summary is recorded in evidence_summary.functional.
No listed criterion applied
OncoKB ↗
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Context only
COSMIC ↗
For specialists
Technical detail
ACMG/AMP criteria under ClinGen PTEN VCEP v3.2.0, with the data and sources behind each one.
29 criteria with recorded statuses: 1 met · 15 not met · 1 not assessed · 12 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_000314.8:c.165-7T>C is an intronic variant in PTEN located at position -7 of the intron 2 splice acceptor region.
This variant is present in gnomAD v4.1 at a grpmax filtering allele frequency of 0.006% (11/1,587,106 alleles), which falls within the PTEN VCEP BS1_Strong range (0.0043%-0.056%), indicating the variant is observed at a population frequency greater than expected for a highly penetrant autosomal dominant disorder.
The variant is classified as Likely benign in ClinVar (VCV000412808) by 5 clinical laboratories, consistent with the population frequency evidence.
SpliceAI predicts no significant splicing impact (max delta score = 0.02), which falls within the benign range for computational splice prediction but is not sufficient alone to apply BP4 under the PTEN VCEP without VarSeak concordance.
No pathogenic computational predictions, functional assay data, segregation evidence, de novo observations, or case-level phenotype data were identified to support pathogenicity for this variant.
The variant does not meet PM2 under PTEN VCEP rules because the South Asian subpopulation frequency (0.0111%) exceeds the VCEP subpopulation threshold of 0.002%.
No criteria match.
Met · 1
BS1 StrongPTEN VCEP v3.2.0 BS1_Strong applies when gnomAD filtering allele frequency is between 0.0043% (0.000043) and 0.056% (0.00056). The gnomAD v4.1 grpmax filtering allele frequency for this variant is 5.997e-05 (0.006%), which falls within the BS1_Strong range. This indicates the variant is observed at a population frequency greater than expected for a highly penetrant autosomal dominant disorder like PTEN hamartoma tumor syndrome. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1 grpmax FAF = 5.997e-05 (0.006%)
- within PTEN VCEP BS1_Strong range (0.0043%-0.056%)
- 11 total alleles across 1
- 587
- 106 chromosomes
Sources
Not met · 15 · evaluated, threshold not reached
PVS1 The variant NM_000314.8:c.165-7T>C is an intronic substitution at position -7, which is not a canonical GT-AG ±1 or ±2 splice site. The PTEN VCEP PVS1 decision tree (v3.2.0) applies only to nonsense, frameshift, canonical splice site disruptions, and CNV deletions. An intronic variant at position -7 falls outside the scope of the PVS1 decision tree. Details ▾Hide ▴
Evidence considered
- Intronic substitution at c.165-7 (intron 2 acceptor region)
- not a canonical ±1
- 2 splice site
- variant class is 'other'
- not a null variant bucket
Sources
PS1 No previously established pathogenic variant has been identified at the same nucleotide position (c.165-7) in PTEN. The ClinVar record for this variant (VCV000412808) carries a Likely benign classification from 5 clinical laboratories, and no pathogenic comparator at this position was found. Details ▾Hide ▴
PS2 No de novo observations (confirmed or assumed) were identified for NM_000314.8:c.165-7T>C in the available evidence. No publications report a de novo occurrence of this variant in a patient with PTEN hamartoma tumor syndrome and no family history. Details ▾Hide ▴
Evidence considered
- No de novo reports found in literature or ClinVar submissions
Still missing
- No systematic de novo search beyond ClinVar-linked publications was performed
PS3 No RNA, mini-gene, or other splicing assay data are available for this intronic variant. The Mighell et al. 2018 (PMID: 29706350) phosphatase activity assay applies to missense variants only; this variant is intronic and has no protein-level consequence. SpliceAI predicts no significant splicing impact (max delta = 0.02). Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.02 (no predicted splice impact)
- Mighell et al. functional assay not applicable (intronic
- not missense)
- no RNA or mini-gene splicing assay data available
Still missing
- No functional splicing assay (RNA or mini-gene) data available for this variant
Sources
PS4 No proband counts or case-control data with PTEN phenotype specificity scores are available for this variant. The ClinVar record lists 5 clinical laboratory submissions classifying it as Likely benign, but no proband-level phenotype data suitable for PTEN VCEP PS4 specificity scoring were identified. Details ▾Hide ▴
Evidence considered
- ClinVar: 5 clinical laboratories classify as Likely benign
- no proband counts or phenotype specificity data available
Still missing
- No proband counts with phenotype specificity scores available
Sources
PM2 Under PTEN VCEP v3.2.0, PM2_Supporting requires total gnomAD allele frequency <0.001% (0.00001) AND subpopulation AF <0.002% (0.00002) when multiple alleles are present. Although the total gnomAD v4.1 AF is 0.00069% (<0.001%), the South Asian subpopulation has AF = 0.0111% (10/90,108 alleles), which exceeds the 0.002% subpopulation threshold. The variant therefore fails PM2 under VCEP rules. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1: total AF = 0.00069%
- South Asian subpopulation AF = 0.0111% (10/90
- 108)
- subpopulation AF exceeds PTEN VCEP PM2 threshold of 0.002%
Sources
PM6 No assumed or confirmed de novo observations were identified for this variant in the available evidence. No publications report a de novo occurrence in a proband with PTEN hamartoma tumor syndrome. Details ▾Hide ▴
Evidence considered
- No de novo reports identified in literature or ClinVar
Still missing
- No systematic de novo search beyond available sources
PP1 No co-segregation data are available for this variant. No publications report segregation analysis in families with this variant and PTEN-associated phenotypes. Details ▾Hide ▴
Evidence considered
- No co-segregation data identified in available evidence
Still missing
- No family segregation studies available
PP3 Under PTEN VCEP v3.2.0, PP3 for splicing variants requires concordance of SpliceAI (scores 0.5-1, pathogenic range) and VarSeak (Class 4-5). The SpliceAI max delta score for this variant is 0.02, which is far below the 0.5 pathogenic threshold and indicates no predicted splicing impact. PP3 is not supported. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.02
- well below PP3 pathogenic threshold of 0.5
- no VarSeak data available
- REVEL not applicable (intronic)
Sources
BA1 PTEN VCEP v3.2.0 BA1 requires gnomAD filtering allele frequency >0.056% (0.00056). The gnomAD v4.1 grpmax filtering allele frequency is 5.997e-05 (0.006%), which is approximately 10-fold below the BA1 threshold. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1 grpmax FAF = 0.006%
- well below BA1 threshold of 0.056%
Sources
BS2 PTEN VCEP v3.2.0 BS2 requires observation in the homozygous state in a healthy or PHTS-unaffected individual. No homozygous observations are present in gnomAD v2.1 or v4.1 (homozygotes = 0 in both datasets). Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: 0 homozygotes
- gnomAD v4.1: 0 homozygotes
- no unaffected homozygous individuals reported
Sources
BS3 No RNA, mini-gene, or other splicing assay data demonstrating no splicing impact are available for this intronic variant. PTEN VCEP BS3_Strong requires a splicing assay showing no impact. The Mighell et al. 2018 phosphatase activity assay (BS3_Supporting) applies to missense variants only. SpliceAI delta of 0.02 alone is insufficient to satisfy the VCEP BS3 functional evidence requirement. Details ▾Hide ▴
Evidence considered
- SpliceAI delta = 0.02 (predicts no splice impact
- but not a functional assay)
- no RNA/mini-gene data
- Mighell assay not applicable (intronic variant)
Still missing
- No functional splicing assay data available
Sources
BS4 No segregation data demonstrating lack of segregation in affected family members are available for this variant. PTEN VCEP BS4 requires two or more families for strong evidence, or one family for supporting evidence. Details ▾Hide ▴
Evidence considered
- No segregation data available in literature or ClinVar submissions
Still missing
- No family segregation studies available
BP2 No observations of this variant in trans with a pathogenic or likely pathogenic PTEN variant, nor three or more observations in cis/phase-unknown with different P/LP PTEN variants, were identified in the available evidence. Details ▾Hide ▴
Evidence considered
- No trans or cis observations with P/LP PTEN variants identified
Still missing
- No phase data available
BP5 PTEN VCEP v3.2.0 BP5 requires at least two cases where the variant is found in individuals with an alternate molecular basis for disease, where the other gene/disorder is highly penetrant and there is no phenotypic overlap with PTEN. No such cases were identified in the available evidence. Details ▾Hide ▴
Evidence considered
- No cases with alternate molecular basis for disease identified
Still missing
- No systematic search for alternate molecular diagnoses in variant carriers
Not assessed · 1 · no assessment recorded
BP4 PTEN VCEP v3.2.0 BP4 requires concordance of BOTH SpliceAI (scores 0-0.2 considered benign) AND VarSeak (Class 1-2 considered benign) predicting no splicing impact. The SpliceAI max delta score is 0.02, which falls within the benign range and would support BP4. However, VarSeak data are not available for this variant, precluding full VCEP-concordant assessment. BP4 cannot be applied without VarSeak data to confirm concordance. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.02 (within benign range 0-0.2)
- VarSeak data unavailable — VCEP requires concordance of both tools
Still missing
- VarSeak splice prediction data not available — required for VCEP BP4 concordance assessment
Sources
Not applicable · 12· recorded as not applicable Show reasons ▾Hide reasons ▴
PM1 N/AThis is an intronic variant (c.165-7) that does not alter any amino acid residue. PTEN VCEP PM1 applies only to variants located in catalytic motifs at residues 90-94 (WPD loop), 123-130 (P-loop), or 166-168 (TI-loop) of NP_000305.3. Details ▾Hide ▴
Evidence considered
- Intronic variant does not affect any amino acid residue
- catalytic motif residues not implicated
Sources
PM3 VCEPAutosomal dominant disorder criterion; PM3 (detected in trans with a pathogenic variant) applies to recessive disorders and is not applicable to PTEN hamartoma tumor syndrome. Details ▾Hide ▴
Evidence considered
- PTEN VCEP: PM3 not applicable (PTEN is an autosomal dominant disorder)
Sources
PM4 N/AIntronic substitution variant; PM4 applies to protein length changes due to in-frame deletions/insertions or stop-loss variants, none of which are relevant to this intronic substitution. Details ▾Hide ▴
Evidence considered
- Substitution variant
- not an in-frame indel or stop-loss variant
PM5 N/AThis is an intronic substitution, not a missense variant. PTEN VCEP PM5 applies only to missense changes at an amino acid residue where a different pathogenic or likely pathogenic missense change has been previously established. Details ▾Hide ▴
Evidence considered
- Intronic variant
- no amino acid residue change
- PM5 candidate search returned not_applicable
Sources
cspec ↗pm5_candidates
PP2 N/AThis is an intronic variant, not a missense variant. PTEN VCEP PP2 applies specifically to missense variants in a gene with a low rate of benign missense variation where missense variants are a common disease mechanism. Details ▾Hide ▴
Evidence considered
- Intronic variant does not meet PP2 prerequisite of being a missense variant
Sources
PP4 VCEPPTEN VCEP v3.2.0: Phenotype specificity has been incorporated into the PS4 rule specifications. PP4 is not applicable under this VCEP. Details ▾Hide ▴
Evidence considered
- VCEP specification: PP4 not applicable
- phenotype specificity addressed within PS4
Sources
PP5 VCEPThis criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee (PTEN VCEP v3.2.0). Details ▾Hide ▴
Evidence considered
- PTEN VCEP v3.2.0: PP5 explicitly marked Not Applicable for this VCEP
Sources
BP1 VCEPPTEN VCEP v3.2.0: This rule is not applicable to PTEN. BP1 (missense variant in a gene where primarily truncating variants cause disease) does not apply because both missense and truncating variants are established disease mechanisms in PTEN. Details ▾Hide ▴
BP3 VCEPIntronic substitution variant; BP3 applies to in-frame deletions/insertions in repetitive regions, which is not relevant to this variant type. Details ▾Hide ▴
Evidence considered
- Substitution variant
- not an in-frame indel in a repetitive region
BP6 VCEPThis criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee (PTEN VCEP v3.2.0). ClinVar classification as Likely benign from 5 laboratories is noted but does not constitute an applicable BP6 criterion under this VCEP. Details ▾Hide ▴
BP7 N/APTEN VCEP v3.2.0 BP7 requires an intronic variant to be positioned at or beyond +7 (donor site) or -21 (acceptor site) relative to the exon boundary. This variant at c.165-7 is located at position -7 in the intron 2 acceptor region, which is within the splice-region (not deep intronic) and does not meet the positional threshold for BP7 applicability. Details ▾Hide ▴
Evidence considered
- Variant at intronic position -7
- PTEN VCEP BP7 requires position at or beyond -21 for acceptor-site intronic variants
Sources
PS5 N/AThis criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee (PTEN VCEP v3.2.0). PP5 (the benign counterpart) is also marked Not Applicable for this VCEP. Details ▾Hide ▴
Evidence considered
- PTEN VCEP v3.2.0: PP5 explicitly marked Not Applicable for this VCEP
Sources
Identifiers
- Gene
- PTEN
- Transcript
- NM_000314.8
- Coding (HGVS c.)
- NM_000314.8:c.165-7T>C
- Protein (HGVS p.)
- NP_000305.3:p.?
- GRCh38
- chr10:87925506 T>C
- GRCh37
- chr10:89685263 T>C
- ClinVar
- 412808
Gene diagram
Every interpreted variant in PTEN, mapped onto the exon structure of NM_000314.8. Select a row to find it on the plot.
PTENNM_000314.8
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 PTEN
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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
11 / 1,587,106 alleles
AF 6.93e-06 · 0 homozygotes · FAF 6e-05
gnomAD v2.1
1 / 236,384 alleles
AF 4.23e-06 · 0 homozygotes
gnomAD-Canada v1.0
0 / 0 alleles
AF 0 · 0 homozygotes · FAF 0
By genetic ancestry
gnomAD v4.1
AF 6.9e-06 · 11 / 1,587,106 alleles · 0 hom · FAF 6e-05
| South Asian10 / 90,108 | 0.00011 |
| Remaining individuals1 / 61,718 | 1.6e-05 |
0 alternate alleles recorded in 8 other groups: Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American, European (non-Finnish).
gnomAD v2.1
AF 4.2e-06 · 1 / 236,384 alleles · 0 hom
| South Asian1 / 29,852 | 3.3e-05 |
0 alternate alleles recorded in 7 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals.
gnomAD-Canada
AF 0 · 0 / 0 alleles · 0 hom
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 6.93085e-06; MAF= 0.00069%, 11/1587106 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000110978; MAF= 0.01110%, 10/90108 alleles, homozygotes = 0); grpmax FAF= 5.997e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 4.2304e-06; MAF= 0.00042%, 1/236384 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.34986e-05; MAF= 0.00335%, 1/29852 alleles, homozygotes = 0).
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
PP3 Under PTEN VCEP v3.2.0, PP3 for splicing variants requires concordance of SpliceAI (scores 0.5-1, pathogenic range) and VarSeak (Class 4-5). The SpliceAI max delta score for this variant is 0.02, which is far below the 0.5 pathogenic threshold and indicates no predicted splicing impact. PP3 is not supported. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.02
- well below PP3 pathogenic threshold of 0.5
- no VarSeak data available
- REVEL not applicable (intronic)
Sources
BP4 PTEN VCEP v3.2.0 BP4 requires concordance of BOTH SpliceAI (scores 0-0.2 considered benign) AND VarSeak (Class 1-2 considered benign) predicting no splicing impact. The SpliceAI max delta score is 0.02, which falls within the benign range and would support BP4. However, VarSeak data are not available for this variant, precluding full VCEP-concordant assessment. BP4 cannot be applied without VarSeak data to confirm concordance. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.02 (within benign range 0-0.2)
- VarSeak data unavailable — VCEP requires concordance of both tools
Still missing
- VarSeak splice prediction data not available — required for VCEP BP4 concordance assessment
Sources
BP7 N/APTEN VCEP v3.2.0 BP7 requires an intronic variant to be positioned at or beyond +7 (donor site) or -21 (acceptor site) relative to the exon boundary. This variant at c.165-7 is located at position -7 in the intron 2 acceptor region, which is within the splice-region (not deep intronic) and does not meet the positional threshold for BP7 applicability. Details ▾Hide ▴
Evidence considered
- Variant at intronic position -7
- PTEN VCEP BP7 requires position at or beyond -21 for acceptor-site intronic variants
Sources
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
9 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 25645574 ↗ACG clinical guideline: Genetic testing and management of hereditary gastrointestinal cancer syndromes.No paper-specific finding is recorded.
-
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.No paper-specific finding is recorded.
-
PMID 15604628 ↗Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors.Trepanier A et al. · 2004No paper-specific finding is recorded.
-
PMID 17392385 ↗American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography.Saslow D et al. · 2007No paper-specific finding is recorded.
-
PMID 20301661 ↗PTEN Hamartoma Tumor Syndrome.Adam MP et al. · 1993No paper-specific finding is recorded.
-
PMID 23519317 ↗Clinical genetics evaluation in identifying the etiology of autism spectrum disorders: 2013 guideline revisions.Schaefer GB et al. · 2013No paper-specific finding is recorded.
-
PMID 23788249 ↗ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.Green RC et al. · 2013No paper-specific finding is recorded.
-
PMID 24493721 ↗American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers.Lu KH et al. · 2014No paper-specific finding is recorded.
-
PMID 28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.No paper-specific finding is recorded.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
11 / 1,587,106 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 Likely benign
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
ClinGen CSpec
Captured ClinGen CSpec source record
Open source ↗
All source links
- ClinGen CSpec ↗cspec.genome.network/cspec/ui/svi/doc/135637575
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/412808/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/10-89685263-T-C?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr10-87925506-T-C?dataset=gn…
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_000314.8%3Ac.165-…
- OncoKB ↗www.oncokb.org/gene/PTEN/?
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=PTEN+c.165-7T%3EC
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= 6.93085e-06; MAF= 0.00069%, 11/1587106 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000110978; MAF= 0.01110%, 10/90108 alleles, homozygotes = 0); grpmax FAF= 5.997e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 4.2304e-06; MAF= 0.00042%, 1/236384 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.34986e-05; MAF= 0.00335%, 1/29852 alleles, homozygotes = 0).
ClinVar
This variant has been reported in ClinVar as Likely benign (5 clinical laboratories). (ClinVarID = 412808)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
Somatic
This variant has not previously been reported in somatic cancers (COSMIC).