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POT1c.1884A>CBenign
Print report
Variant interpretation report

POT1 c.1884A>C, p.(Thr628=)

NM_015450.3:c.1884A>C NP_056265.2:p.(Thr628=) View identifiers
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.

About POT1

No gene-level summary was recorded for this case.

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
BA1Stand alone
BA1 · stand alone

NM_015450.3:c.1884A>C is present at an allele frequency exceeding 1% in gnomAD. In gnomAD v2.1, the total AF is 1.07% (2980/279114 alleles) with 157 homozygotes observed. The grpmax filtering AF is 10.72% in the African/African American population. In gnomAD v4.1, the total AF is 0.59% with 477 homozygotes, and the grpmax FAF is 11.04%. The total AF in v2.1 exceeds the 1% BA1 threshold and is far above the ACMG/AMP 2015 threshold of 5% in the highest subpopulation. This frequency is incompatible with a rare Mendelian disease-causing variant.

BP6Supporting
BP6 · supporting

NM_015450.3:c.1884A>C is classified as Benign in ClinVar by 7 clinical laboratories (6 reporting 'Benign', 1 reporting 'benign'). Although individual submissions have review status 'criteria provided, single submitter', the concordance across multiple independent clinical laboratories provides supporting evidence for a benign classification.

BP7Supporting
BP7 · supporting

NM_015450.3:c.1884A>C is a synonymous variant (p.Thr628=). SpliceAI predicts no impact on splicing (max delta score = 0.00). The nucleotide is not highly conserved, as evidenced by the high population frequency (>10% in the African/African American population). BP7 criteria are satisfied: synonymous variant with no predicted splice impact at a non-conserved nucleotide.

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, BP6 supporting benign, BP7 supporting benign; combination = 1 stand-alone 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
9,370 / 1,588,362 alleles

gnomAD v4.1: 9,370 / 1,588,362 alleles. Recorded AF 0.00589916. Recorded homozygote count 477.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 0.0106766; MAF= 1.06766%, 2980/279114 alleles, homozygotes = 157) and has highest observed frequency in the African/African American population (AF= 0.110954; MAF= 11.09536%, 2739/24686 alleles, homozygotes = 156); grpmax FAF= 0.107247.

gnomAD-Canada

This variant is present in gnomAD-Canada v1.0 (AF= 0.0068403908794788275, 126/18420 alleles, homozygotes = 9).

Applied · BA1 →
gnomAD v4.1 ↗gnomAD v2.1 ↗gnomAD-Canada ↗
SpliceAI score
0.000 maximum delta

Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.

Applied · BP7 → SpliceAI ↗
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
COSMIC ↗Cancer Hotspots ↗
For specialists

Technical detail

ACMG/AMP criteria under Not recorded, with the data and sources behind each one.

26 criteria with recorded statuses: 3 met · 16 not met · 2 not assessed · 5 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic
PVS1PS1PS2PS3PS4PM1PM2PM5PM6PP1PP2PP3PP4PP5PS5
Benign
BA1BS1BS2BS3BS4BP1BP2BP4BP5BP6BP7
Met Not met Not assessed Not applicable

NM_015450.3:c.1884A>C is a synonymous variant (p.Thr628=) in POT1 classified as Benign based on the ACMG/AMP 2015 guidelines.

This variant is present at high frequency in population databases: gnomAD v2.1 reports an allele frequency of 1.07% (2980/279114 alleles, 157 homozygotes), with the highest subpopulation frequency of 11.1% in the African/African American population (grpmax FAF 10.7%); gnomAD v4.1 reports an allele frequency of 0.59% (9370/1588362 alleles, 477 homozygotes), with grpmax FAF of 11.0%. This frequency meets the stand-alone benign criterion BA1.

ClinVar classifies this variant as Benign based on consensus from 7 clinical laboratories (ClinVar variation ID: 475068), providing supporting evidence for a benign classification (BP6).

SpliceAI predicts no impact on splicing (max delta score = 0.00), and the high population frequency indicates the nucleotide is not conserved, satisfying BP7 for this synonymous variant.

No variant-specific functional studies, de novo observations, segregation data, or case-control evidence were identified for this variant. The ClinVar-cited publications (PMID:25741868, PMID:26467025, PMID:28492532) are methodology and guideline papers that do not mention NM_015450.3:c.1884A>C.

Met · 3

BA1 Stand aloneNM_015450.3:c.1884A>C is present at an allele frequency exceeding 1% in gnomAD. In gnomAD v2.1, the total AF is 1.07% (2980/279114 alleles) with 157 homozygotes observed. The grpmax filtering AF is 10.72% in the African/African American population. In gnomAD v4.1, the total AF is 0.59% with 477 homozygotes, and the grpmax FAF is 11.04%. The total AF in v2.1 exceeds the 1% BA1 threshold and is far above the ACMG/AMP 2015 threshold of 5% in the highest subpopulation. This frequency is incompatible with a rare Mendelian disease-causing variant. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1 total AF=1.07% (2980/279114 alleles
  • 157 homozygotes)
  • grpmax FAF=10.72% (African/African American). gnomAD v4.1 total AF=0.59% (9370/1588362 alleles
  • 477 homozygotes)
  • grpmax FAF=11.04% (African/African American). Absent from gnomAD-Canada.
Sources
gnomad_v2 ↗gnomad_v4 ↗generic_acmg_combination_rules
BP6 SupportingNM_015450.3:c.1884A>C is classified as Benign in ClinVar by 7 clinical laboratories (6 reporting 'Benign', 1 reporting 'benign'). Although individual submissions have review status 'criteria provided, single submitter', the concordance across multiple independent clinical laboratories provides supporting evidence for a benign classification. Details ▾Hide ▴
Evidence considered
  • ClinVar classifies as Benign by 7 clinical laboratories (GeneDx
  • Ambry Genetics
  • Rigshospitalet
  • Quest Diagnostics
  • Labcorp/Invitae
  • Breakthrough Genomics
  • Sinai Health System
  • Mayo Clinic). ClinVar variation ID: 475068.
Sources
clinvar ↗
BP7 SupportingNM_015450.3:c.1884A>C is a synonymous variant (p.Thr628=). SpliceAI predicts no impact on splicing (max delta score = 0.00). The nucleotide is not highly conserved, as evidenced by the high population frequency (>10% in the African/African American population). BP7 criteria are satisfied: synonymous variant with no predicted splice impact at a non-conserved nucleotide. Details ▾Hide ▴
Evidence considered
  • Synonymous variant p.(Thr628=)
  • SpliceAI max delta 0.00 (no predicted donor/acceptor gain or loss)
  • gnomAD grpmax FAF 10.7-11.0% indicates the nucleotide is not highly conserved.
Sources
spliceai ↗gnomad_v2 ↗gnomad_v4 ↗

Not met · 16 · evaluated, threshold not reached

PS2 No de novo observation data are available for NM_015450.3:c.1884A>C. PS2 requires confirmation of de novo occurrence with both maternity and paternity confirmed. Details ▾Hide ▴
Evidence considered
  • No de novo data identified in ClinVar
  • literature
  • or case evidence.
Still missing
  • No de novo testing data available.
PS3 No variant-specific functional studies have been performed for NM_015450.3:c.1884A>C. The ClinVar-cited publications (PMID:25741868, PMID:26467025) are methodology papers that do not contain any experimental data for this variant. Details ▾Hide ▴
Evidence considered
  • No well-established in vitro or in vivo functional studies identified for this variant.
Still missing
  • No variant-specific functional assays available.
PS4 No case-control or prevalence data demonstrate a statistically significant enrichment of NM_015450.3:c.1884A>C in affected individuals compared to controls. The variant is common in the general population, which is inconsistent with a pathogenic role. Details ▾Hide ▴
Evidence considered
  • Variant is present at high frequency in gnomAD (v2.1 AF=1.07%
  • v4.1 AF=0.59%)
  • inconsistent with pathogenic enrichment.
Still missing
  • No case-control study available.
Sources
gnomad_v2 ↗gnomad_v4 ↗
PM1 NM_015450.3:c.1884A>C is not located in a statistically significant mutational hotspot or a critical functional domain where benign variation is absent. Details ▾Hide ▴
Evidence considered
  • Hotspot analysis confirms residue is not significant and the exact variant is not listed in curated hotspot databases.
PM2 NM_015450.3:c.1884A>C is common in population databases. In gnomAD v2.1, total allele frequency is 1.07% (2980/279114 alleles) with 157 homozygotes, exceeding the PM2 threshold of <0.1%. In gnomAD v4.1, AF is 0.59% (9370/1588362 alleles) with 477 homozygotes. Highest subpopulation frequency is 11.1% in African/African American (v2.1). This variant is far too common to apply PM2. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1 total AF=1.07% (2980/279114
  • 157 homozygotes)
  • gnomAD v4.1 total AF=0.59% (9370/1588362
  • 477 homozygotes)
  • African/African American subpopulation AF=11.1% (v2.1)
  • 11.2% (v4.1).
Sources
gnomad_v2 ↗gnomad_v4 ↗
PM6 No de novo observation data are available for NM_015450.3:c.1884A>C. PM6 requires confirmation of de novo occurrence with maternity and paternity confirmed. Details ▾Hide ▴
Evidence considered
  • No de novo data identified.
Still missing
  • No de novo testing data available.
PP1 No co-segregation data are available for NM_015450.3:c.1884A>C. PP1 requires evidence of co-segregation with disease in multiple affected family members. Details ▾Hide ▴
Evidence considered
  • No co-segregation or family study data identified.
Still missing
  • No segregation data available.
PP3 In silico tools do not predict a damaging effect for NM_015450.3:c.1884A>C. REVEL score is 0.039 (low, predicted benign). SpliceAI max delta is 0.00 (no predicted splicing impact). Multiple lines of computational evidence suggest no functional consequence. Details ▾Hide ▴
Evidence considered
  • REVEL score 0.039 (predicted benign)
  • SpliceAI max delta 0.00 (no splicing impact). Multiple computational tools predict no damaging effect.
Sources
revelspliceai ↗
PP4 No patient phenotype or clinical syndrome specificity data are available for NM_015450.3:c.1884A>C. PP4 requires the variant to be observed in a patient whose phenotype or family history is highly specific for the disease. Details ▾Hide ▴
Evidence considered
  • No phenotype-specific data for this variant.
Still missing
  • No detailed phenotype data available.
PP5 ClinVar classifies NM_015450.3:c.1884A>C as Benign, not Pathogenic. No reputable source has reported this variant as pathogenic. PP5 requires a reputable source to report the variant as pathogenic with evidence unavailable for independent evaluation. Details ▾Hide ▴
Evidence considered
  • ClinVar classification: Benign (7 clinical laboratories). No reputable source reports as pathogenic.
Sources
clinvar ↗
BS2 BS2 requires observation in a healthy adult individual for a disorder with full penetrance expected at an early age. POT1 tumor predisposition syndrome (POT1-TPDS) is an adult-onset cancer predisposition syndrome with incomplete penetrance and variable expressivity. The presence of 157-477 homozygotes in gnomAD does not satisfy BS2 because the disorder does not have full penetrance at an early age. Details ▾Hide ▴
Evidence considered
  • POT1-TPDS is an adult-onset cancer predisposition syndrome with incomplete penetrance
  • does not meet BS2 'full penetrance expected at early age' requirement despite 157 homozygotes (v2.1) and 477 homozygotes (v4.1).
Sources
gnomad_v2 ↗gnomad_v4 ↗
BS3 No variant-specific functional studies have been performed for NM_015450.3:c.1884A>C demonstrating no damaging effect on protein function or splicing. The ClinVar-cited publications (PMID:25741868, PMID:26467025) are methodology papers that contain no experimental data for this variant. Details ▾Hide ▴
Evidence considered
  • No well-established functional studies demonstrating no damaging effect for this variant.
Still missing
  • No variant-specific functional studies available.
BS4 No data on lack of segregation are available for NM_015450.3:c.1884A>C. BS4 requires observation of the variant in a family member without the disease phenotype. Details ▾Hide ▴
Evidence considered
  • No segregation data available.
Still missing
  • No family segregation data available.
BP2 No data are available regarding co-occurrence of NM_015450.3:c.1884A>C in trans with a pathogenic POT1 variant (for a dominant disorder) or in cis with a pathogenic variant. Details ▾Hide ▴
Evidence considered
  • No data on in trans or in cis co-occurrence with pathogenic variants.
Still missing
  • No phase data available.
BP5 No evidence is available that NM_015450.3:c.1884A>C is found in a case with an alternate molecular basis for disease. BP5 requires observation in a patient with an established alternative genetic cause. Details ▾Hide ▴
Evidence considered
  • No alternate molecular basis data identified.
Still missing
  • No data on alternate molecular diagnoses in carriers.
PS5 ClinVar classifies NM_015450.3:c.1884A>C as Benign (7 clinical laboratories). No reputable source has reported this variant as pathogenic. Details ▾Hide ▴
Evidence considered
  • ClinVar classification: Benign (6 clinical laboratories)
  • benign (1 clinical laboratory)
  • no reputable source reports as pathogenic.
Sources
clinvar ↗

Not assessed · 2 · no assessment recorded

BS1 BS1 is superseded by BA1, which provides a stronger level of evidence (stand-alone benign vs. strong benign). The allele frequency already meets BA1 criteria; applying BS1 in addition would double-count the same population frequency evidence. Details ▾Hide ▴
Evidence considered
  • Superseded by BA1.
BP4 BP4 is not applied because BP7 is the more specific criterion for synonymous variants. BP4 and BP7 should not both be used for the same variant per ACMG/AMP 2015 guidelines, as they both rely on computational evidence. BP7 is applied instead. Details ▾Hide ▴
Evidence considered
  • BP7 applied instead of BP4 to avoid double-counting computational evidence for a synonymous variant.
Not applicable · 5· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANM_015450.3:c.1884A>C is a synonymous variant (p.Thr628=) with no predicted amino acid change; PVS1 applies only to null variants (nonsense, frameshift, canonical splice). The ClinGen SVI PVS1 framework (PMC6185798) confirms this variant does not fall into a null-variant bucket. Details ▾Hide ▴
Evidence considered
  • Synonymous variant producing p.(Thr628=)
  • pvs1_variant_assessment confirms variant_bucket='other' and apply_generic_pvs1_framework=false.
Sources
pvs1_variant_assessmentpvs1_gene_context
PS1 N/APS1 requires an alternate nucleotide change at the same position with an established pathogenic classification. This synonymous variant has no known pathogenic missense comparator at c.1884. Details ▾Hide ▴
Evidence considered
  • No alternate pathogenic nucleotide change identified at c.1884.
PM5 N/APM5 requires a known pathogenic missense variant at the same amino acid residue. NM_015450.3:c.1884A>C is a synonymous variant (p.Thr628=) with no amino acid change, so there is no residue context for a missense comparator. pm5_candidates confirms not_applicable. Details ▾Hide ▴
Evidence considered
  • Synonymous variant
  • no amino acid residue to compare. pm5_candidates confirms recommendation level 'not_applicable'.
Sources
pm5_candidates
PP2 N/APP2 applies to missense variants in genes where missense variants are a common disease mechanism and benign missense variation is rare. NM_015450.3:c.1884A>C is a synonymous variant (p.Thr628=), not a missense variant. Details ▾Hide ▴
Evidence considered
  • Synonymous variant
  • PP2 is specific to missense variants.
BP1 N/ABP1 applies to missense variants in genes where the primary disease mechanism is through truncating variants. NM_015450.3:c.1884A>C is a synonymous variant (p.Thr628=), not a missense variant. Details ▾Hide ▴
Evidence considered
  • Synonymous variant
  • BP1 is specific to missense variants.

Identifiers

Gene
POT1
Transcript
NM_015450.3
Coding (HGVS c.)
NM_015450.3:c.1884A>C
Protein (HGVS p.)
NP_056265.2:p.(Thr628=)
GRCh38
chr7:124823983 T>G
GRCh37
chr7:124464037 T>G
ClinVar
475068

Gene diagram

Every interpreted variant in POT1, mapped onto the exon structure of NM_015450.3. Select a row to find it on the plot.

POT1NM_015450.3
Fetching transcript structure from UCSC…
gnomAD v4.1 9,370 / 1,588,362 alleles AF 0.0059 · 477 homozygotes · FAF 0.11
gnomAD v2.1 2,980 / 279,114 alleles AF 0.0107 · 157 homozygotes · FAF 0.107
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 0.0059 · 9370 / 1,588,362 alleles · 477 hom · FAF 0.11
African/African American8348 / 74,256 0.11461 hom
Admixed American432 / 59,626 0.00723 hom
Remaining individuals437 / 61,574 0.007112 hom
Middle Eastern21 / 6,006 0.0035
South Asian24 / 90,052 0.000271 hom
European (non-Finnish)108 / 1,158,002 9.3e-05
0 alternate alleles recorded in 4 other groups: European (Finnish), Amish, East Asian, Ashkenazi Jewish.

gnomAD v2.1

AF 0.011 · 2980 / 279,114 alleles · 157 hom · FAF 0.11
African/African American2739 / 24,686 0.11156 hom
Admixed American174 / 34,542 0.0051 hom
Remaining individuals32 / 7,058 0.0045
South Asian9 / 30,028 0.0003
European (non-Finnish)26 / 127,698 0.0002
0 alternate alleles recorded in 3 other groups: Ashkenazi Jewish, East Asian, European (Finnish).

gnomAD-Canada

AF not recorded · ? / ? alleles

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 0.00589916; MAF= 0.58992%, 9370/1588362 alleles, homozygotes = 477) and has highest observed frequency in the African/African American population (AF= 0.112422; MAF= 11.24219%, 8348/74256 alleles, homozygotes = 461); grpmax FAF= 0.110405.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 0.0106766; MAF= 1.06766%, 2980/279114 alleles, homozygotes = 157) and has highest observed frequency in the African/African American population (AF= 0.110954; MAF= 11.09536%, 2739/24686 alleles, homozygotes = 156); grpmax FAF= 0.107247.

gnomAD-Canada

This variant is present in gnomAD-Canada v1.0 (AF= 0.0068403908794788275, 126/18420 alleles, homozygotes = 9).

Open the gnomAD-Canada detail page →

SpliceAI and Pangolin

Pangolin splice lossmagnitude shown
-0.000
Pangolin splice gain
0.050

Other predictors

REVEL
0.039
BayesDel
Not available

How the predictions were used

BP7 SupportingNM_015450.3:c.1884A>C is a synonymous variant (p.Thr628=). SpliceAI predicts no impact on splicing (max delta score = 0.00). The nucleotide is not highly conserved, as evidenced by the high population frequency (>10% in the African/African American population). BP7 criteria are satisfied: synonymous variant with no predicted splice impact at a non-conserved nucleotide. Details ▾Hide ▴
Evidence considered
  • Synonymous variant p.(Thr628=)
  • SpliceAI max delta 0.00 (no predicted donor/acceptor gain or loss)
  • gnomAD grpmax FAF 10.7-11.0% indicates the nucleotide is not highly conserved.
Sources
spliceai ↗gnomad_v2 ↗gnomad_v4 ↗
PP3 In silico tools do not predict a damaging effect for NM_015450.3:c.1884A>C. REVEL score is 0.039 (low, predicted benign). SpliceAI max delta is 0.00 (no predicted splicing impact). Multiple lines of computational evidence suggest no functional consequence. Details ▾Hide ▴
Evidence considered
  • REVEL score 0.039 (predicted benign)
  • SpliceAI max delta 0.00 (no splicing impact). Multiple computational tools predict no damaging effect.
Sources
revelspliceai ↗
BP4 BP4 is not applied because BP7 is the more specific criterion for synonymous variants. BP4 and BP7 should not both be used for the same variant per ACMG/AMP 2015 guidelines, as they both rely on computational evidence. BP7 is applied instead. Details ▾Hide ▴
Evidence considered
  • BP7 applied instead of BP4 to avoid double-counting computational evidence for a synonymous variant.

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.039.

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

  • 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. · 2015
    This is the foundational ACMG/AMP sequence variant interpretation guideline. It provides the classification framework and criteria definitions but does not discuss NM_015450.3:c.1884A>C or any specific POT1 variant.
    Does not name this variant
    PMID 25741868 ↗
  • A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.
    Karbassi I et al. · 2016
    Describes a standardized DNA variant scoring system for pathogenicity assessment in Mendelian disorders based on prediction tools, population frequency, co-occurrence, segregation, and functional studies. Does not mention NM_015450.3:c.1884A>C or any specific POT1 variant.
    Does not name this variant
    PMID 26467025 ↗
  • 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. · 2015
    Provides practice guidelines for referral indications for cancer predisposition assessment. Discusses general genetic counseling approaches for hereditary cancer syndromes but does not mention NM_015450.3:c.1884A>C or any POT1 variants.
    Does not name this variant
    PMID 25394175 ↗
  • POT1 Tumor Predisposition.
    Adam MP et al. · 1993
    GeneReviews entry for POT1 tumor predisposition syndrome. Summarizes the clinical characteristics, diagnosis, and management of POT1-TPDS at the gene level but does not discuss the specific variant NM_015450.3:c.1884A>C.
    Does not name this variant
    PMID 33119245 ↗
  • Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
    Nykamp K et al. · 2017
    Presents Sherloc, a refined variant classification system based on the ACMG-AMP framework. Provides classification methodology and criteria refinement but does not mention NM_015450.3:c.1884A>C or discuss any specific POT1 variant.
    Does not name this variant
    PMID 28492532 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

gnomAD v4.1 9,370 / 1,588,362 recorded alleles Open source ↗
gnomAD v2.1 Captured gnomAD v2.1 source record Open source ↗
SpliceAI Lookup Recorded maximum delta 0.000 Open source ↗
ClinVar 6 Benign · 1 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

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= 0.00589916; MAF= 0.58992%, 9370/1588362 alleles, homozygotes = 477) and has highest observed frequency in the African/African American population (AF= 0.112422; MAF= 11.24219%, 8348/74256 alleles, homozygotes = 461); grpmax FAF= 0.110405.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 0.0106766; MAF= 1.06766%, 2980/279114 alleles, homozygotes = 157) and has highest observed frequency in the African/African American population (AF= 0.110954; MAF= 11.09536%, 2739/24686 alleles, homozygotes = 156); grpmax FAF= 0.107247.

gnomAD-Canada

This variant is present in gnomAD-Canada v1.0 (AF= 0.0068403908794788275, 126/18420 alleles, homozygotes = 9).

ClinVar

This variant has been reported in ClinVar as Benign (6 clinical laboratories) and as benign (1 clinical laboratory). (ClinVarID = 475068)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.039.

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.