0%
PTCH1c.4251C>TLikely benign
Print report
Variant interpretation report

PTCH1 c.4251C>T, p.(His1417=)

NM_000264.5:c.4251C>T NP_000255.2:p.(His1417=) View identifiers
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.

About PTCH1

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: 1 Benign evidence criteria: 3
Pathogenic criteria applied · 1
PM2Supporting
PM2 · supporting

NM_000264.5:c.4251C>T is present at extremely low frequency in population databases, below the 0.1% PM2 threshold for non-VCEP generic ACMG. gnomAD v2.1: 10/282,784 alleles (AF=0.0035%); gnomAD v4.1: 50/1,614,202 alleles (AF=0.0031%); gnomAD-Canada: 0 alleles. No homozygotes observed.

Benign criteria applied · 3
BP4Supporting
BP4 · supporting

Multiple lines of computational evidence suggest no impact on the gene product. SpliceAI predicts no splicing alteration (max delta score 0.00). REVEL score is 0.27, in the neutral range. The variant is synonymous (p.His1417=) with no predicted effect on splicing or protein function.

BP6Supporting
BP6 · supporting

ClinVar classifies NM_000264.5:c.4251C>T as Likely benign, supported by 5 clinical laboratories (Ambry Genetics, Invitae/Labcorp, Copenhagen University Hospital, PreventionGenetics, CeGaT). Multiple reputable clinical testing laboratories have independently reached a benign interpretation.

BP7Supporting
BP7 · supporting

NM_000264.5:c.4251C>T is a synonymous variant (p.His1417=) in exon 23. SpliceAI predicts no splicing impact (max delta 0.00). The nucleotide is not located at a highly conserved position predicted to affect splicing. BP7 is met for a synonymous variant with no predicted splice effect.

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: PM2 supporting, BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; combination = 1 supporting + 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
50 / 1,614,202 alleles

gnomAD v4.1: 50 / 1,614,202 alleles. Recorded AF 3.09751e-05. Recorded homozygote count 0.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 3.53627e-05; MAF= 0.00354%, 10/282784 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 8.46501e-05; MAF= 0.00847%, 3/35440 alleles, homozygotes = 0); grpmax FAF= 1.686e-05.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

Applied · PM2 →
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 · BP4, 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.

27 criteria with recorded statuses: 4 met · 5 not met · 12 not assessed · 6 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic
PVS1PS1PS2PS3PS4PM1PM2PM5PM6PP1PP2PP3PP4PP5PS5
Benign
BA1BS1BS2BS3BS4BP1BP2BP3BP4BP5BP6BP7
Met Not met Not assessed Not applicable

NM_000264.5:c.4251C>T is a synonymous variant (p.His1417=) in exon 23 of PTCH1. SpliceAI predicts no splicing impact (max delta 0.00) and REVEL score is 0.27 in the neutral range, consistent with no functional effect.

The variant is present at very low frequency in population databases: 10/282,784 alleles in gnomAD v2.1 (AF=0.0035%) and 50/1,614,202 alleles in gnomAD v4.1 (AF=0.0031%), with no homozygotes observed.

ClinVar classifies this variant as Likely benign, supported by 5 independent clinical testing laboratories. No reputable source reports this variant as pathogenic.

Seven publications were reviewed for variant-specific evidence, including the ACMG/AMP 2015 guidelines (PMID:25741868), Sherloc refinement (PMID:28492532), GeneReviews NBCCS overview (PMID:20301330), and Gorlin syndrome clinical utility gene card (PMID:21304560). None mention NM_000264.5:c.4251C>T specifically.

Application of ACMG/AMP 2015 generic combination rules: three supporting benign criteria (BP4, BP6, BP7) and one supporting pathogenic criterion (PM2) are met. The preponderance of evidence supports a Likely benign classification.

Met · 4

PM2 SupportingNM_000264.5:c.4251C>T is present at extremely low frequency in population databases, below the 0.1% PM2 threshold for non-VCEP generic ACMG. gnomAD v2.1: 10/282,784 alleles (AF=0.0035%); gnomAD v4.1: 50/1,614,202 alleles (AF=0.0031%); gnomAD-Canada: 0 alleles. No homozygotes observed. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1 AF=0.00354% (10/282
  • 784 alleles)
  • gnomAD v4.1 AF=0.00310% (50/1
  • 614
  • 202 alleles)
  • Absent from gnomAD-Canada
  • No homozygotes observed in any population database
Sources
gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗
BP4 SupportingMultiple lines of computational evidence suggest no impact on the gene product. SpliceAI predicts no splicing alteration (max delta score 0.00). REVEL score is 0.27, in the neutral range. The variant is synonymous (p.His1417=) with no predicted effect on splicing or protein function. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta: 0.00 (no splicing impact)
  • REVEL score: 0.27 (neutral range)
  • Synonymous variant with no predicted functional consequence
Sources
revelspliceai ↗
BP6 SupportingClinVar classifies NM_000264.5:c.4251C>T as Likely benign, supported by 5 clinical laboratories (Ambry Genetics, Invitae/Labcorp, Copenhagen University Hospital, PreventionGenetics, CeGaT). Multiple reputable clinical testing laboratories have independently reached a benign interpretation. Details ▾Hide ▴
Evidence considered
  • ClinVar: Likely benign
  • 5 clinical laboratories (ClinVar ID 132735)
  • Submitting labs: Ambry Genetics
  • Invitae
  • Rigshospitalet Copenhagen
  • PreventionGenetics
  • CeGaT
Sources
clinvar ↗
BP7 SupportingNM_000264.5:c.4251C>T is a synonymous variant (p.His1417=) in exon 23. SpliceAI predicts no splicing impact (max delta 0.00). The nucleotide is not located at a highly conserved position predicted to affect splicing. BP7 is met for a synonymous variant with no predicted splice effect. Details ▾Hide ▴
Evidence considered
  • Synonymous variant p.His1417=
  • SpliceAI max delta: 0.00 (no splicing impact predicted)
  • No evidence of altered splicing
Sources
spliceai ↗

Not met · 5 · evaluated, threshold not reached

PP3 In silico predictors do not support a deleterious effect. REVEL score is 0.27 (neutral range, below typical pathogenic threshold of 0.5). SpliceAI max delta score is 0.00 (no splicing impact predicted). No computational evidence supports pathogenicity. Details ▾Hide ▴
Evidence considered
  • REVEL score: 0.27 (neutral range)
  • SpliceAI max delta: 0.00 (no splice impact)
Sources
revelspliceai ↗
PP5 PP5 requires a reputable source to report the variant as pathogenic. ClinVar classifies NM_000264.5:c.4251C>T as Likely benign from 5 clinical laboratories. No expert panel or reputable source has classified this variant as pathogenic. All reviewed publications are general guidelines or gene-level reviews that do not assert pathogenicity for this variant. Details ▾Hide ▴
Evidence considered
  • ClinVar: Likely benign (5 clinical laboratories)
  • No reputable source reports as pathogenic
Sources
clinvar ↗
BA1 Allele frequency in gnomAD is far below the 1% BA1 threshold. gnomAD v2.1 AF=0.00354% (10/282,784); gnomAD v4.1 AF=0.00310% (50/1,614,202). BA1 requires allele frequency >1% in any population. Details ▾Hide ▴
Evidence considered
  • Maximum population AF: 0.00847% (Admixed American
  • gnomAD v2.1)
  • Far below 1% BA1 threshold
Sources
gnomad_v2 ↗gnomad_v4 ↗
BS1 Allele frequency is below the 0.3% BS1 threshold for non-VCEP generic ACMG. Maximum population AF is 0.00847% in Admixed American population (gnomAD v2.1). Does not meet BS1. Details ▾Hide ▴
Evidence considered
  • Maximum population AF: 0.00847% (Admixed American
  • gnomAD v2.1)
  • Below 0.3% BS1 threshold
Sources
gnomad_v2 ↗gnomad_v4 ↗
PS5 PS5 requires a reputable source to report the variant as pathogenic. ClinVar classifies NM_000264.5:c.4251C>T as Likely benign (5 clinical laboratories, ClinVar ID 132735). No source asserts pathogenicity for this variant. Details ▾Hide ▴
Evidence considered
  • ClinVar classification: Likely benign from 5 clinical laboratories
  • no submissions classify as pathogenic
Sources
clinvar ↗

Not assessed · 12 · no assessment recorded

PS2 No de novo data are available for NM_000264.5:c.4251C>T. No publications or ClinVar submissions report de novo occurrence for this variant. Details ▾Hide ▴
Still missing
  • No de novo testing data available
PS3 No variant-specific functional studies were identified for NM_000264.5:c.4251C>T. PMID:25741868 (ACMG guidelines) was reviewed as the sole PS3-candidate paper but does not contain any variant-specific functional data. Details ▾Hide ▴
Evidence considered
  • PMID:25741868 reviewed — ACMG/AMP guidelines paper
  • does not mention c.4251C>T or any variant-specific functional assay
Still missing
  • No functional studies available for this variant
PS4 No variant-specific case-control or cohort prevalence data were identified. All PS4-candidate papers (PMID:15604628, 20301330, 21304560, 25741868, 26389258, 26389333, 28492532) are general guidelines or gene-level reviews that do not report variant-specific prevalence statistics. Details ▾Hide ▴
Evidence considered
  • Multiple guideline and review papers reviewed
  • none provide variant-specific case-control data for c.4251C>T
Still missing
  • No variant-specific prevalence or case-control data
PM1 Residue p.His1417 is not located in a statistically significant mutational hotspot (evidence_brief confirms hotspot analysis negative). No established critical functional domain encompasses this position. Insufficient evidence to invoke PM1. Details ▾Hide ▴
Evidence considered
  • Hotspot analysis negative
  • residue not in statistically significant cluster
  • No critical functional domain annotation for this position
Still missing
  • No functional domain annotation supporting PM1
PM6 No de novo data are available for NM_000264.5:c.4251C>T. No publications or ClinVar submissions report de novo occurrence for this variant. Details ▾Hide ▴
Still missing
  • No de novo testing data available
PP1 No co-segregation data are available for NM_000264.5:c.4251C>T. No family studies or segregation analyses were identified in the literature or ClinVar submissions. Details ▾Hide ▴
Still missing
  • No co-segregation data available
PP4 No patient phenotype or family history data were provided for assessment. PP4 requires that the patient's phenotype or family history is highly specific for the gene/disease. Details ▾Hide ▴
Still missing
  • No patient phenotype data provided
BS2 No specific evidence of observation in healthy adults beyond population database allele counts. BS2 requires documented observation in a healthy adult individual with full penetrance expected at an early age. No such clinical reports were identified. Details ▾Hide ▴
Still missing
  • No documented observation in healthy adults beyond population databases
BS3 No variant-specific functional studies were identified for NM_000264.5:c.4251C>T demonstrating no damaging effect. PMID:25741868 was reviewed as the sole BS3-candidate paper but does not contain any variant-specific functional data. Details ▾Hide ▴
Evidence considered
  • PMID:25741868 reviewed — ACMG/AMP guidelines paper
  • does not mention c.4251C>T or any variant-specific functional assay
Still missing
  • No functional studies available for this variant
BS4 No non-segregation data are available for NM_000264.5:c.4251C>T. No family studies demonstrating lack of segregation with disease were identified. Details ▾Hide ▴
Still missing
  • No non-segregation data available
BP2 No data are available on observation of NM_000264.5:c.4251C>T in trans with a known pathogenic PTCH1 variant. No such observations were reported in ClinVar or the literature. Details ▾Hide ▴
Still missing
  • No trans-phase observation data available
BP5 No evidence of an alternate molecular basis for disease was identified in the case. BP5 requires that an alternative causative variant has been identified in the patient. No such data were provided. Details ▾Hide ▴
Still missing
  • No data on alternate molecular basis
Not applicable · 6· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANM_000264.5:c.4251C>T is a synonymous variant (p.His1417=) in exon 23. It does not fall into any PVS1 null-variant bucket (nonsense, frameshift, canonical splice ±1,2, initiation codon, single/multi-exon deletion). PVS1 decision algorithm does not trigger for synonymous variants. Details ▾Hide ▴
Evidence considered
  • Synonymous variant p.His1417=
  • not predicted to cause loss of function
  • PTCH1 LOF mechanism is supported for PVS1 gene-level eligibility but variant does not qualify
Sources
pvs1_gene_contextpvs1_variant_assessmentpvs1_generic_framework ↗
PS1 N/ASynonymous variant with no amino acid change. PS1 requires the same amino acid change as a previously established pathogenic variant. Not applicable for synonymous changes. Details ▾Hide ▴
Evidence considered
  • Synonymous variant p.His1417=
  • no amino acid change to compare
PM5 N/ANM_000264.5:c.4251C>T is a synonymous variant (p.His1417=) with no amino acid change. PM5 requires a different pathogenic missense change at the same residue. No missense comparator candidates were identified, and PM5 semantics cannot be applied to a synonymous change. Details ▾Hide ▴
Evidence considered
  • Synonymous variant
  • no amino acid residue change
  • PM5 candidate harvesting confirmed not applicable
Sources
pm5_candidates
PP2 N/APP2 applies to missense variants in genes where missense variation is an established disease mechanism and benign missense variation is rare. NM_000264.5:c.4251C>T is a synonymous variant (p.His1417=), not a missense change. Details ▾Hide ▴
Evidence considered
  • Synonymous variant
  • PP2 requires a missense change
BP1 N/ABP1 applies to missense variants in genes where truncating variants are a known disease mechanism. NM_000264.5:c.4251C>T is a synonymous variant (p.His1417=), not a missense change. Details ▾Hide ▴
Evidence considered
  • Synonymous variant
  • BP1 requires a missense change
BP3 N/ASkipped per adjudication instructions: variant type is substitution (not in-frame indel). Details ▾Hide ▴

No further detail was recorded.

Identifiers

Gene
PTCH1
Transcript
NM_000264.5
Coding (HGVS c.)
NM_000264.5:c.4251C>T
Protein (HGVS p.)
NP_000255.2:p.(His1417=)
GRCh38
chr9:95447005 G>A
GRCh37
chr9:98209287 G>A
ClinVar
701613, 132735

Gene diagram

Every interpreted variant in PTCH1, mapped onto the exon structure of NM_000264.5. Select a row to find it on the plot.

PTCH1NM_000264.5
Fetching transcript structure from UCSC…
gnomAD v4.1 50 / 1,614,202 alleles AF 3.1e-05 · 0 homozygotes · FAF 2.83e-05
gnomAD v2.1 10 / 282,784 alleles AF 3.54e-05 · 0 homozygotes · FAF 1.69e-05
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 3.1e-05 · 50 / 1,614,202 alleles · 0 hom · FAF 2.8e-05
European (non-Finnish)44 / 1,180,036 3.7e-05
Admixed American2 / 60,032 3.3e-05
African/African American2 / 75,058 2.7e-05
South Asian2 / 91,088 2.2e-05
0 alternate alleles recorded in 6 other groups: Remaining individuals, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish.

gnomAD v2.1

AF 3.5e-05 · 10 / 282,784 alleles · 0 hom · FAF 1.7e-05
Admixed American3 / 35,440 8.5e-05
African/African American1 / 24,956 4e-05
European (non-Finnish)5 / 129,106 3.9e-05
South Asian1 / 30,616 3.3e-05
0 alternate alleles recorded in 4 other groups: Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals.

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 3.09751e-05; MAF= 0.00310%, 50/1614202 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.7287e-05; MAF= 0.00373%, 44/1180036 alleles, homozygotes = 0); grpmax FAF= 2.826e-05.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 3.53627e-05; MAF= 0.00354%, 10/282784 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 8.46501e-05; MAF= 0.00847%, 3/35440 alleles, homozygotes = 0); grpmax FAF= 1.686e-05.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

Pangolin splice lossmagnitude shown
-0.010
Pangolin splice gain
0.000

Other predictors

REVEL
0.270
BayesDel
Not available

How the predictions were used

BP4 SupportingMultiple lines of computational evidence suggest no impact on the gene product. SpliceAI predicts no splicing alteration (max delta score 0.00). REVEL score is 0.27, in the neutral range. The variant is synonymous (p.His1417=) with no predicted effect on splicing or protein function. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta: 0.00 (no splicing impact)
  • REVEL score: 0.27 (neutral range)
  • Synonymous variant with no predicted functional consequence
Sources
revelspliceai ↗
BP7 SupportingNM_000264.5:c.4251C>T is a synonymous variant (p.His1417=) in exon 23. SpliceAI predicts no splicing impact (max delta 0.00). The nucleotide is not located at a highly conserved position predicted to affect splicing. BP7 is met for a synonymous variant with no predicted splice effect. Details ▾Hide ▴
Evidence considered
  • Synonymous variant p.His1417=
  • SpliceAI max delta: 0.00 (no splicing impact predicted)
  • No evidence of altered splicing
Sources
spliceai ↗
PP3 In silico predictors do not support a deleterious effect. REVEL score is 0.27 (neutral range, below typical pathogenic threshold of 0.5). SpliceAI max delta score is 0.00 (no splicing impact predicted). No computational evidence supports pathogenicity. Details ▾Hide ▴
Evidence considered
  • REVEL score: 0.27 (neutral range)
  • SpliceAI max delta: 0.00 (no splice impact)
Sources
revelspliceai ↗

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.27.

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

  • 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
    ACMG/AMP 2015 standards and guidelines for the interpretation of sequence variants. A general framework paper that defines the classification criteria used in this assessment. Does not mention NM_000264.5:c.4251C>T or any PTCH1-specific variant.
    Does not name this variant
    PMID 25741868 ↗
  • Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors.
    Trepanier A et al. · 2004
    National Society of Genetic Counselors recommendations for cancer genetic risk assessment and counseling. A general practice guideline; does not discuss NM_000264.5:c.4251C>T or specific PTCH1 variants.
    Does not name this variant
    PMID 15604628 ↗
  • Nevoid Basal Cell Carcinoma Syndrome.
    Adam MP et al. · 1993
    GeneReviews overview of Nevoid Basal Cell Carcinoma Syndrome (Gorlin syndrome). Summarizes PTCH1 as the primary gene for NBCCS and describes clinical features and genetic testing approaches. Does not mention NM_000264.5:c.4251C>T.
    Does not name this variant
    PMID 20301330 ↗
  • Clinical utility gene card for: Gorlin syndrome.
    Lo Muzio L et al. · 2011
    Clinical utility gene card for Gorlin syndrome summarizing PTCH1 gene-level testing indications, diagnostic criteria, and analytical sensitivity. Does not mention NM_000264.5:c.4251C>T or any individual PTCH1 variants.
    Does not name this variant
    PMID 21304560 ↗
  • Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version.
    PDQ Cancer Genetics Editorial Board · 2002
    PDQ Cancer Genetics Risk Assessment and Counseling summary from the National Cancer Institute. A general educational resource on cancer genetic counseling. Does not discuss NM_000264.5:c.4251C>T or specific PTCH1 variants.
    Does not name this variant
    PMID 26389258 ↗
  • Genetics of Skin Cancer (PDQ®): Health Professional Version.
    PDQ Cancer Genetics Editorial Board · 2002
    PDQ Genetics of Skin Cancer summary covering Gorlin syndrome and PTCH1 at the gene level. Provides general information on skin cancer genetics. Does not mention NM_000264.5:c.4251C>T.
    Does not name this variant
    PMID 26389333 ↗
  • Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
    Nykamp K et al. · 2017
    Sherloc refinement of the ACMG-AMP variant classification criteria. Provides a systematic framework for applying ACMG/AMP rules. Does not mention NM_000264.5:c.4251C>T or any PTCH1-specific 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 50 / 1,614,202 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 5 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

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= 3.09751e-05; MAF= 0.00310%, 50/1614202 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.7287e-05; MAF= 0.00373%, 44/1180036 alleles, homozygotes = 0); grpmax FAF= 2.826e-05.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 3.53627e-05; MAF= 0.00354%, 10/282784 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 8.46501e-05; MAF= 0.00847%, 3/35440 alleles, homozygotes = 0); grpmax FAF= 1.686e-05.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

This variant has been reported in ClinVar as Likely benign (5 clinical laboratories). (ClinVarID = 132735)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.27.

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.