About PMS2
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
PMS2 c.2566C>T, p.(Leu856=)
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 ClinGen PMS2 VCEP v2.0.0. 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: 1
Benign evidence criteria: 2
Pathogenic criteria applied · 1
PM2Supporting
PM2 · supporting
NM_000535.7:c.2566C>T is extremely rare in population databases. The variant is absent from gnomAD v2.1 and present in gnomAD v4.1 at an allele frequency of 5.057e-06 (5/988,724 alleles, no homozygotes), which is below the PMS2 VCEP v2.0.0 PM2_Supporting threshold of <0.00002 (<1 in 50,000 alleles). The grpmax filtering allele frequency is 1.39e-06.
Benign criteria applied · 2
BP4Supporting
BP4 · supporting
NM_000535.7:c.2566C>T is a synonymous variant and SpliceAI predicts no splicing impact (max delta score = 0.00), which satisfies the PMS2 VCEP v2.0.0 BP4_Supporting rule for intronic and synonymous variants (SpliceAI delta score <= 0.1). The HCI prior branch of BP4 does not apply as this is not a missense variant.
BP7Supporting
BP7 · supporting
NM_000535.7:c.2566C>T is a synonymous (silent) variant located in exon 15 of PMS2 (c.2446-c.*2474) at position c.2566, which is +120 nucleotides downstream of the splice acceptor site. This is beyond the +7 position from the 3' exon boundary, satisfying the PMS2 VCEP v2.0.0 BP7 rule for synonymous variants at or beyond -21/+7 (5'/3' exonic). The variant does not lie within the critical splice consensus region.
Recorded classification: Likely benign
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PMS2 Version 2.0.0 v2.0.0 criteria-combination framework: matched Rule19 (Benign.Supporting >=2) with applied criteria: PM2 supporting, BP4 supporting benign, BP7 supporting benign; 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
5 / 988,724 alleles
gnomAD v4.1: 5 / 988,724 alleles. Recorded AF 5.05702e-06. Recorded homozygote count 0.
gnomAD v2.1
Absent from gnomAD v2.1.
SpliceAI score
0.000 maximum delta
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
5 reported laboratory submissions
4 Likely benign · 1 Benign.
Context only
ClinVar ↗
Functional evidence
Statement recorded
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
No listed criterion applied
OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
Context only
For specialists
Technical detail
ACMG/AMP criteria under ClinGen PMS2 VCEP v2.0.0, with the data and sources behind each one.
26 criteria with recorded statuses: 3 met · 11 not met · 0 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_000535.7:c.2566C>T (p.Leu856=) is a synonymous variant in exon 15 of PMS2. It is extremely rare in population databases, with an allele frequency of 5.057e-06 in gnomAD v4.1 (5/988,724 alleles, no homozygotes) and absent from gnomAD v2.1, satisfying PM2_Supporting per PMS2 VCEP v2.0.0.
SpliceAI predicts no splicing impact for this variant (max delta = 0.00), satisfying BP4_Supporting per PMS2 VCEP v2.0.0 for synonymous variants.
The variant is a synonymous substitution located at c.2566 in exon 15, +120 nucleotides from the splice acceptor site, well beyond the +7 position defined by the BP7 rule. BP7_Supporting is met per PMS2 VCEP v2.0.0.
PVS1, PS1, and PM5 are not applicable as this is a synonymous variant producing no amino acid change. PS4, PM1, PM6, PP2, PP5, BP1, BP2, and BP6 are not applicable per the PMS2 VCEP v2.0.0 specifications.
No de novo observations (PS2), functional studies (PS3, BS3), cosegregation data (PP1, BS4), trans co-occurrence data (BS2), tumor pathology data (PP4, BP5), or computational evidence supporting pathogenicity (PP3) were identified for this variant.
This variant has been reported in ClinVar as Likely benign by four clinical laboratories and Benign by one clinical laboratory (ClinVar ID 701564). In ClinVar, submissions cited methodology papers without variant-specific clinical evidence.
Under the PMS2 VCEP v2.0.0 combination rules, the presence of two benign supporting criteria (BP4_Supporting, BP7_Supporting) satisfies Rule19 (>=2 Benign.Supporting -> Likely Benign). PM2_Supporting is also met but does not alter the classification under the VCEP rule hierarchy.
No criteria match.
Met · 3
PM2 SupportingNM_000535.7:c.2566C>T is extremely rare in population databases. The variant is absent from gnomAD v2.1 and present in gnomAD v4.1 at an allele frequency of 5.057e-06 (5/988,724 alleles, no homozygotes), which is below the PMS2 VCEP v2.0.0 PM2_Supporting threshold of <0.00002 (<1 in 50,000 alleles). The grpmax filtering allele frequency is 1.39e-06. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1: AF=5.057e-06 (5/988
- 724 alleles
- 0 homozygotes)
- grpmax FAF=1.39e-06. gnomAD v2.1: absent. gnomAD-Canada: absent.
Sources
BP4 SupportingNM_000535.7:c.2566C>T is a synonymous variant and SpliceAI predicts no splicing impact (max delta score = 0.00), which satisfies the PMS2 VCEP v2.0.0 BP4_Supporting rule for intronic and synonymous variants (SpliceAI delta score <= 0.1). The HCI prior branch of BP4 does not apply as this is not a missense variant. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.00
- confirming no predicted splicing impact. Synonymous variant meets VCEP BP4_Supporting threshold.
Sources
BP7 SupportingNM_000535.7:c.2566C>T is a synonymous (silent) variant located in exon 15 of PMS2 (c.2446-c.*2474) at position c.2566, which is +120 nucleotides downstream of the splice acceptor site. This is beyond the +7 position from the 3' exon boundary, satisfying the PMS2 VCEP v2.0.0 BP7 rule for synonymous variants at or beyond -21/+7 (5'/3' exonic). The variant does not lie within the critical splice consensus region. Details ▾Hide ▴
Evidence considered
- Synonymous variant at c.2566 in exon 15
- located +120 from splice acceptor (beyond +7 threshold). SpliceAI max delta = 0.00 confirms no cryptic splice effect.
Sources
Not met · 11 · evaluated, threshold not reached
PS2 No de novo occurrences of NM_000535.7:c.2566C>T were identified in the literature or curated de novo databases. Per PMS2 VCEP v2.0.0, PS2 requires documented de novo observation with assigned point values. Details ▾Hide ▴
Evidence considered
- Targeted exploratory search for de novo data found no evidence for this variant.
Still missing
- No dedicated de novo database query was performed
- ClinGen de novo registry may contain additional data.
PS3 No well-established functional studies demonstrating a damaging effect of NM_000535.7:c.2566C>T on PMS2 protein function or splicing were identified. The PMS2 VCEP functional assay documentation spreadsheet does not include this variant. As a synonymous variant, functional impact would require evidence of aberrant splicing, which SpliceAI does not predict (max delta = 0.00). Details ▾Hide ▴
Evidence considered
- SpliceAI predicts no splicing impact (max delta = 0.00). No functional studies identified in VCEP functional assay documentation or literature.
Still missing
- No minigene splicing assay or MMR functional assay has been performed for this variant.
Sources
PP1 No cosegregation data in affected family members were identified for NM_000535.7:c.2566C>T. Per PMS2 VCEP v2.0.0, PP1 requires combined Bayes Likelihood Ratio exceeding defined thresholds in pedigrees with disease. Details ▾Hide ▴
Evidence considered
- Targeted literature search found no cosegregation studies for this variant.
Still missing
- No family-based segregation analysis has been published for this variant.
PP3 PP3 per PMS2 VCEP v2.0.0 requires either a missense variant with HCI prior probability >0.68, or a predicted splice defect for non-canonical splicing nucleotides with SpliceAI delta >= 0.2. NM_000535.7:c.2566C>T is a synonymous variant not present in the HCI prior lookup table (which is populated only for missense substitutions), and SpliceAI predicts no splicing impact (max delta = 0.00). Neither PP3 branch is satisfied. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.00 (below 0.2 threshold). HCI prior not found (synonymous variant
- not in missense lookup table).
Sources
PP4 No CRC/endometrial MSI-H tumors or loss of MMR protein expression consistent with this variant location were identified for NM_000535.7:c.2566C>T. Per PMS2 VCEP v2.0.0, PP4 requires documented MSI-H tumors and/or MMR protein expression loss. Details ▾Hide ▴
Evidence considered
- No tumor pathology or IHC data identified for this variant.
Still missing
- No tumor studies with MSI/IHC correlating to this variant have been reported.
BA1 BA1 per PMS2 VCEP v2.0.0 requires gnomAD v4 grpmax filtering allele frequency >= 0.0028 (0.28%). The observed grpmax FAF for NM_000535.7:c.2566C>T is 1.39e-06, well below the BA1 threshold. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1 grpmax FAF = 1.39e-06
- far below BA1 threshold of 0.0028.
Sources
BS1 BS1 per PMS2 VCEP v2.0.0 requires gnomAD v4 grpmax filtering allele frequency >= 0.00028 and < 0.0028. The observed grpmax FAF for NM_000535.7:c.2566C>T is 1.39e-06, which is below the lower BS1 bound of 0.00028. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1 grpmax FAF = 1.39e-06
- below BS1 threshold of 0.00028.
Sources
BS2 No reports of NM_000535.7:c.2566C>T observed in trans with a known pathogenic PMS2 variant in a patient with colorectal cancer after age 45 and no evidence of CMMRD were identified. Per PMS2 VCEP v2.0.0, BS2 requires documented co-occurrence in trans with confirmation of phase. Details ▾Hide ▴
Evidence considered
- No trans co-occurrence reports with known pathogenic PMS2 variants were identified.
Still missing
- No phase-confirmed trans data available.
BS3 No well-established functional studies demonstrating no damaging effect of NM_000535.7:c.2566C>T were identified. Per PMS2 VCEP v2.0.0, BS3 requires calibrated functional assays with odds for pathogenicity <= 0.05, or synonymous variants with no mRNA aberration demonstrated by laboratory assay. No such studies have been published for this variant. ClinVar classification as Likely benign is not a functional assay. Details ▾Hide ▴
Evidence considered
- No functional studies (MMR activity
- splicing assays
- mRNA analysis) identified for this specific variant.
Still missing
- No MMR functional assay or mRNA splicing analysis has been performed for this variant.
Sources
BS4 No dedicated segregation studies demonstrating lack of cosegregation with disease were identified for NM_000535.7:c.2566C>T. Per PMS2 VCEP v2.0.0, BS4 requires combined Bayes Likelihood Ratio < 0.05 from pedigree analysis. Details ▾Hide ▴
Evidence considered
- No family-based segregation studies identified for this variant.
Still missing
- No formal cosegregation analysis available.
BP5 No tumor pathology data (MSS tumors, BRAF V600E, MLH1 methylation) were identified for NM_000535.7:c.2566C>T. Per PMS2 VCEP v2.0.0, BP5 requires documented CRC/endometrial tumors with MSS and/or no loss of MMR protein expression, or BRAF V600E/MLH1 methylation findings. Details ▾Hide ▴
Evidence considered
- No tumor-level evidence identified for this variant.
Still missing
- No tumor pathology or MSI/IHC studies have been correlated with this variant.
Not applicable · 12· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/APVS1 is not applicable to synonymous variants. NM_000535.7:c.2566C>T is a synonymous substitution (p.Leu856=) and does not introduce a premature termination codon, disrupt the initiation codon, or affect a canonical splice site. Per PMS2 VCEP v2.0.0, PVS1 applies only to null variants (nonsense, frameshift, canonical splice, or large genomic alterations). Details ▾Hide ▴
Evidence considered
- Synonymous variant NP_000526.2:p.(Leu856=) does not meet any PVS1 null-variant bucket per ClinGen SVI PVS1 framework.
Sources
PS1 N/APS1 requires a predicted missense substitution that encodes the same amino acid change as a previously established Pathogenic variant. NM_000535.7:c.2566C>T is a synonymous variant with no amino acid change; therefore PS1 is not applicable. Details ▾Hide ▴
Evidence considered
- Synonymous variant (p.Leu856=) does not produce an amino acid change.
Sources
PS4 VCEPPS4 is listed as Not Applicable in the PMS2 VCEP v2.0.0 specifications. Details ▾Hide ▴
Evidence considered
- Criterion explicitly marked Not Applicable by the InSiGHT VCEP for PMS2.
Sources
PM1 VCEPPM1 is listed as Not Applicable in the PMS2 VCEP v2.0.0 specifications. Details ▾Hide ▴
Evidence considered
- Criterion explicitly marked Not Applicable by the InSiGHT VCEP for PMS2.
Sources
PM5 N/APM5 requires a missense change at an amino acid residue where a different missense change was classified as Pathogenic. NM_000535.7:c.2566C>T is a synonymous variant (p.Leu856=) and does not alter the amino acid; therefore PM5 is not applicable. Details ▾Hide ▴
Evidence considered
- Synonymous variant does not qualify as a missense change at any amino acid residue.
Sources
cspec ↗pm5_candidates
PM6 VCEPPM6 is listed as Not Applicable in the PMS2 VCEP v2.0.0 specifications. Details ▾Hide ▴
Evidence considered
- Criterion explicitly marked Not Applicable by the InSiGHT VCEP for PMS2.
Sources
PP2 VCEPPP2 is listed as Not Applicable in the PMS2 VCEP v2.0.0 specifications. Details ▾Hide ▴
Evidence considered
- Criterion explicitly marked Not Applicable by the InSiGHT VCEP for PMS2.
Sources
PP5 VCEPPP5 is listed as Not Applicable in the PMS2 VCEP v2.0.0 specifications. Details ▾Hide ▴
Evidence considered
- Criterion explicitly marked Not Applicable by the InSiGHT VCEP for PMS2.
Sources
BP1 VCEPBP1 is listed as Not Applicable in the PMS2 VCEP v2.0.0 specifications. Details ▾Hide ▴
Evidence considered
- Criterion explicitly marked Not Applicable by the InSiGHT VCEP for PMS2.
Sources
BP2 VCEPBP2 is listed as Not Applicable in the PMS2 VCEP v2.0.0 specifications. Details ▾Hide ▴
Evidence considered
- Criterion explicitly marked Not Applicable by the InSiGHT VCEP for PMS2.
Sources
BP6 VCEPBP6 is listed as Not Applicable in the PMS2 VCEP v2.0.0 specifications. Details ▾Hide ▴
Evidence considered
- Criterion explicitly marked Not Applicable by the InSiGHT VCEP for PMS2.
Sources
PS5 N/APS5 applies to variants with the same amino acid change as a previously established pathogenic variant. NM_000535.7:c.2566C>T is a synonymous variant (p.Leu856=) with no amino acid change; therefore PS5 is not applicable. Details ▾Hide ▴
Evidence considered
- Synonymous variant produces no amino acid change.
Identifiers
- Gene
- PMS2
- Transcript
- NM_000535.7
- Coding (HGVS c.)
- NM_000535.7:c.2566C>T
- Protein (HGVS p.)
- NP_000526.2:p.(Leu856=)
- GRCh38
- chr7:5973422 G>A
- GRCh37
- chr7:6013053 G>A
- ClinVar
- 2774118, 1792847, 701564
Gene diagram
Every interpreted variant in PMS2, mapped onto the exon structure of NM_000535.7. Select a row to find it on the plot.
PMS2NM_000535.7
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 PMS2
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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
5 / 988,724 alleles
AF 5.06e-06 · 0 homozygotes · FAF 1.39e-06
gnomAD v2.1
Allele count data not recorded
gnomAD-Canada v1.0
0 / 0 alleles
AF 0 · 0 homozygotes · FAF 0
By genetic ancestry
gnomAD v4.1
AF 5.1e-06 · 5 / 988,724 alleles · 0 hom · FAF 1.4e-06
| Remaining individuals1 / 41,228 | 2.4e-05 |
| European (non-Finnish)4 / 671,666 | 6e-06 |
0 alternate alleles recorded in 8 other groups: Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.
gnomAD-Canada
AF 0 · 0 / 0 alleles · 0 hom
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 5.05702e-06; MAF= 0.00051%, 5/988724 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 2.42554e-05; MAF= 0.00243%, 1/41228 alleles, homozygotes = 0); grpmax FAF= 1.39e-06.
gnomAD v2.1
Absent from gnomAD v2.1.
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
BP4 SupportingNM_000535.7:c.2566C>T is a synonymous variant and SpliceAI predicts no splicing impact (max delta score = 0.00), which satisfies the PMS2 VCEP v2.0.0 BP4_Supporting rule for intronic and synonymous variants (SpliceAI delta score <= 0.1). The HCI prior branch of BP4 does not apply as this is not a missense variant. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.00
- confirming no predicted splicing impact. Synonymous variant meets VCEP BP4_Supporting threshold.
Sources
BP7 SupportingNM_000535.7:c.2566C>T is a synonymous (silent) variant located in exon 15 of PMS2 (c.2446-c.*2474) at position c.2566, which is +120 nucleotides downstream of the splice acceptor site. This is beyond the +7 position from the 3' exon boundary, satisfying the PMS2 VCEP v2.0.0 BP7 rule for synonymous variants at or beyond -21/+7 (5'/3' exonic). The variant does not lie within the critical splice consensus region. Details ▾Hide ▴
Evidence considered
- Synonymous variant at c.2566 in exon 15
- located +120 from splice acceptor (beyond +7 threshold). SpliceAI max delta = 0.00 confirms no cryptic splice effect.
Sources
PP3 PP3 per PMS2 VCEP v2.0.0 requires either a missense variant with HCI prior probability >0.68, or a predicted splice defect for non-canonical splicing nucleotides with SpliceAI delta >= 0.2. NM_000535.7:c.2566C>T is a synonymous variant not present in the HCI prior lookup table (which is populated only for missense substitutions), and SpliceAI predicts no splicing impact (max delta = 0.00). Neither PP3 branch is satisfied. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta = 0.00 (below 0.2 threshold). HCI prior not found (synonymous variant
- not in missense lookup table).
Sources
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
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
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PMID 25741868 ↗Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.Richards S et al. · 2015No paper-specific finding is recorded.
-
PMID 20301390 ↗Lynch Syndrome.Adam MP et al. · 1993No paper-specific finding is recorded.
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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.
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PMID 25356965 ↗ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing.ACMG Board of Directors · 2015No paper-specific finding is recorded.
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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. · 2015No paper-specific finding is recorded.
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PMID 27854360 ↗Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics.Kalia SS et al. · 2017No paper-specific finding is recorded.
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PMID 34012068 ↗ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG).Miller DT et al. · 2021No paper-specific finding is recorded.
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PMID 34043773 ↗European guidelines from the EHTG and ESCP for Lynch syndrome: an updated third edition of the Mallorca guidelines based on gene and gender.Seppälä TT et al. · 2021No paper-specific finding is recorded.
-
PMID 28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.Nykamp K et al. · 2017No paper-specific finding is recorded.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
5 / 988,724 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
4 Likely 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 ↗
ClinGen CSpec
Captured ClinGen CSpec source record
Open source ↗
All source links
- ClinGen CSpec ↗cspec.genome.network/cspec/ui/svi/doc/1578297058
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/701564/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/7-6013053-G-A?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr7-5973422-G-A?dataset=gnomad_r4
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_000535.7%3Ac.2566…
- OncoKB ↗www.oncokb.org/gene/PMS2/L856=
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=PMS2+c.2566C%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= 5.05702e-06; MAF= 0.00051%, 5/988724 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 2.42554e-05; MAF= 0.00243%, 1/41228 alleles, homozygotes = 0); grpmax FAF= 1.39e-06.
gnomAD v2.1
Absent from gnomAD v2.1.
ClinVar
This variant has been reported in ClinVar as Likely benign (4 clinical laboratories) and as Benign (1 clinical laboratory). (ClinVarID = 701564)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
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.