About PTEN
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
PTEN c.253+1G>A, p.?
Classification
Pathogenic
Variant description:
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is pathogenic. Select a step to read what it means.
Pathogenic.A pathogenic 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 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: 4
Benign evidence criteria: 0
Pathogenic criteria applied · 4
PVS1Very strong
PVS1 · very strong
Canonical +1 splice donor variant (c.253+1G>A) in PTEN intron 4. Per the PTEN VCEP decision tree (NM_000314.8), canonical GT-AG ±1,2 splice site disruptions at or 5' to p.D375 (c.1121) are assigned PVS1. This variant is far 5' of p.D375, and exon 4 skipping with frameshift p.(Ala72Thrfs*5) and predicted NMD was confirmed by RT-PCR in patient-derived lymphoblastoid cells.
PS1Strong
PS1 · strong
A different nucleotide change at the same position, c.253+1G>T, has been established as pathogenic in family N4 with complete cosegregation with Cowden disease. SpliceAI predicts a donor loss delta score of 0.99 for c.253+1G>A, consistent with impact equal to the known pathogenic c.253+1G>T variant, satisfying the PTEN VCEP PS1 rule for same-nucleotide-position splice variants.
PS3Strong
PS3 · strong
PMID:28677221 (Chen et al. 2017) characterized c.253+1G>A in patient-derived lymphoblastoid cells by RT-PCR, demonstrating exon 4 skipping resulting in frameshift p.(Ala72Thrfs*5). PTEN protein expression was significantly decreased (~50% reduction) and downstream P-AKT was significantly increased in the splice-altered group, satisfying the PTEN VCEP PS3 Strong rule for RNA or other assay demonstrating impact on splicing.
PM2Supporting
PM2 · supporting
c.253+1G>A is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, satisfying the PTEN VCEP PM2_Supporting threshold of allele frequency <0.00001 (0.001%).
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Pathogenic
Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework: matched Rule1 (1 Pathogenic.Very Strong + Pathogenic.Strong >=1) with applied criteria: PVS1 very strong, PS1 strong, PS3 strong, PM2 supporting; maps to Pathogenic.
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
Not recorded
gnomAD v4.1 allele counts were not recorded for this variant.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI score
0.990 maximum delta
Recorded SpliceAI maximum delta score: 0.990. Refer to the recorded PP3/BP4 rationale for interpretation.
No listed criterion applied
SpliceAI ↗
ClinVar submissions
7 reported laboratory submissions
7 Pathogenic.
Context only
ClinVar ↗
No screenshot for this evidence
Functional evidence
Not recorded
No standalone functional evidence summary is recorded in evidence_summary.functional.
Somatic evidence
8 recorded samples
This variant has previously been reported in somatic cancers (COSMIC; COSV64289910, n = 8 times).
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.
26 criteria with recorded statuses: 4 met · 8 not met · 6 not assessed · 8 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
c.253+1G>A is a canonical +1 splice donor variant in PTEN intron 4. Per the PTEN VCEP PVS1 decision tree, canonical GT-AG splice site disruptions at or 5' to p.D375 (c.1121) qualify for PVS1 at very strong strength.
Functional characterization in patient-derived lymphoblastoid cells (PMID:28677221) demonstrated that c.253+1G>A causes exon 4 skipping, resulting in a frameshift (p.Ala72Thrfs*5) with predicted NMD. PTEN protein expression was significantly decreased and P-AKT was significantly increased, satisfying PS3 at strong strength per PTEN VCEP specifications.
A different nucleotide substitution at the same position, c.253+1G>T, has been established as pathogenic with complete cosegregation with Cowden disease in family N4 (PMID:9259288). SpliceAI predicts a donor loss delta of 0.99 for c.253+1G>A, indicating impact equal to the known pathogenic variant, satisfying PS1 at strong strength.
c.253+1G>A is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, satisfying PM2 at supporting strength (allele frequency <0.001% per PTEN VCEP).
This variant has been reported in ClinVar as Pathogenic by 7 clinical laboratories (ClinVar Variation ID: 7820) and has been observed in somatic cancers (COSMIC, n=8).
Combined classification: PVS1 (very_strong) + PS1 (strong) + PS3 (strong) + PM2 (supporting). Under the ACMG/AMP 2015 combining rules per the PTEN VCEP framework, Rule 1 is satisfied: one very strong criterion (PVS1) plus at least one strong criterion (PS1, PS3) → Pathogenic.
No criteria match.
Met · 4
PVS1 Very strongCanonical +1 splice donor variant (c.253+1G>A) in PTEN intron 4. Per the PTEN VCEP decision tree (NM_000314.8), canonical GT-AG ±1,2 splice site disruptions at or 5' to p.D375 (c.1121) are assigned PVS1. This variant is far 5' of p.D375, and exon 4 skipping with frameshift p.(Ala72Thrfs*5) and predicted NMD was confirmed by RT-PCR in patient-derived lymphoblastoid cells. Details ▾Hide ▴
Evidence considered
- Canonical +1 splice donor site disruption (GT→AT) in intron 4
- Position c.253+1 is 5' to p.D375 (c.1121) threshold in the PTEN VCEP decision tree
- PMID:28677221 confirms exon 4 skipping → p.(Ala72Thrfs*5) → NMD predicted
- PTEN protein expression significantly decreased
- P-AKT significantly increased in splice-altered group
Sources
PS1 StrongA different nucleotide change at the same position, c.253+1G>T, has been established as pathogenic in family N4 with complete cosegregation with Cowden disease. SpliceAI predicts a donor loss delta score of 0.99 for c.253+1G>A, consistent with impact equal to the known pathogenic c.253+1G>T variant, satisfying the PTEN VCEP PS1 rule for same-nucleotide-position splice variants. Details ▾Hide ▴
Evidence considered
- PMID:9259288 reports c.253+1G>T as pathogenic splice site mutation with complete cosegregation with Cowden disease in family N4
- SpliceAI max delta 0.99 (donor loss 0.99) for c.253+1G>A predicts impact equal to c.253+1G>T
- PMID:28677221 confirms both c.253+1G>T and c.253+1G>A independently cause exon 4 skipping
Sources
PS3 StrongPMID:28677221 (Chen et al. 2017) characterized c.253+1G>A in patient-derived lymphoblastoid cells by RT-PCR, demonstrating exon 4 skipping resulting in frameshift p.(Ala72Thrfs*5). PTEN protein expression was significantly decreased (~50% reduction) and downstream P-AKT was significantly increased in the splice-altered group, satisfying the PTEN VCEP PS3 Strong rule for RNA or other assay demonstrating impact on splicing. Details ▾Hide ▴
Evidence considered
- RT-PCR from patient LBLs confirms exon 4 skipping for c.253+1G>A
- Predicted protein change: p.(Ala72Thrfs*5) — frameshift with premature termination
- PTEN protein significantly decreased (~50%) in splice-change group vs no-change group
- P-AKT significantly increased in splice-change group
- consistent with loss of PTEN function
Sources
PM2 Supportingc.253+1G>A is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, satisfying the PTEN VCEP PM2_Supporting threshold of allele frequency <0.00001 (0.001%). Details ▾Hide ▴
Evidence considered
- Absent from gnomAD v2.1 (0 alleles)
- Absent from gnomAD v4.1 (0 alleles)
- Absent from gnomAD-Canada v1.0 (0 alleles)
Sources
Not met · 8 · evaluated, threshold not reached
PM1 c.253+1G>A is an intronic splice site variant in intron 4. The PTEN VCEP defines PM1-applicable catalytic motifs as residues 90-94 (WPD loop), 123-130 (P-loop), and 166-168 (TI-loop) of NP_000305.3. This variant does not lie within any of these catalytic motif residues. Details ▾Hide ▴
Evidence considered
- Intronic variant at c.253+1
- not within catalytic motifs at residues 90-94
- 123-130
- or 166-168
Sources
BA1 c.253+1G>A is absent from all gnomAD populations. The PTEN VCEP BA1 threshold is filtering allele frequency >0.00056 (0.056%), which is not met. Details ▾Hide ▴
Evidence considered
- Allele frequency 0 in gnomAD v2.1
- v4.1
- and gnomAD-Canada
Sources
BS1 c.253+1G>A is absent from all gnomAD populations. The PTEN VCEP BS1 threshold is filtering allele frequency from 0.000043 to 0.00056 (0.0043% to 0.056%), which is not met. Details ▾Hide ▴
Evidence considered
- Allele frequency 0 in all gnomAD populations
Sources
BS2 No observations of c.253+1G>A in the homozygous state in healthy or PHTS-unaffected individuals. The PTEN VCEP BS2 requires homozygous observations for application. Details ▾Hide ▴
Evidence considered
- No homozygous observations in gnomAD (hom = null)
Sources
BS3 Functional studies (PMID:28677221) demonstrate a damaging splicing effect for c.253+1G>A (exon 4 skipping, decreased PTEN protein, increased P-AKT). BS3 requires demonstration of no damaging effect on protein function or splicing, which is contradicted by the available evidence. Details ▾Hide ▴
Evidence considered
- PMID:28677221 demonstrates exon 4 skipping and functional impact — opposite of BS3 requirement
Sources
BP2 No observations of c.253+1G>A in trans with a pathogenic or likely pathogenic PTEN variant, nor in cis with different pathogenic/likely pathogenic PTEN variants. The PTEN VCEP BP2 requires such observations. Details ▾Hide ▴
Still missing
- No phase data for this variant
BP4 PTEN VCEP BP4 for splicing variants requires SpliceAI scores of 0-0.2 (evidence of benign) with VarSeak concordance. SpliceAI max delta for c.253+1G>A is 0.99, predicting a strong splicing impact, which contradicts BP4 application. Additionally, functional data (PMID:28677221) confirms splicing disruption. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.99 contradicts benign splicing prediction
- PMID:28677221 confirms exon 4 skipping and functional impact
Sources
BP5 No evidence was identified of c.253+1G>A occurring in a case with an alternate molecular basis for disease. The PTEN VCEP BP5 requires at least two such cases with a highly penetrant alternate gene/disorder and no phenotypic overlap with PTEN. Details ▾Hide ▴
No further detail was recorded.
Not assessed · 6 · no assessment recorded
PS2 No de novo observations with confirmed maternity and paternity were identified in the reviewed literature for c.253+1G>A. Details ▾Hide ▴
Still missing
- No de novo data available for this variant
PS4 Multiple probands with c.253+1G>A have been reported (PMID:28677221: 1 patient; PMID:20600018: 1 patient with numerous GI polyps; ClinVar: 7 clinical laboratories reporting Pathogenic). However, PTEN VCEP PS4 requires specificity scoring based on detailed phenotype data, which is not available from the reviewed sources. Without computable specificity scores, PS4 strength cannot be assigned. Details ▾Hide ▴
Evidence considered
- PMID:28677221: 1 CS patient with c.253+1G>A
- PMID:20600018: 1 PTEN mutation carrier with c.253+1G>A and numerous GI polyps
- ClinVar: 7 clinical laboratories classify as Pathogenic
Still missing
- Detailed phenotype data needed for PTEN specificity scoring
Sources
PM6 No assumed or confirmed de novo observations for c.253+1G>A were identified in the reviewed literature. Details ▾Hide ▴
Still missing
- No de novo observations reported
PP1 No co-segregation data are available for c.253+1G>A specifically. While c.253+1G>T at the same position showed complete cosegregation in family N4 (PMID:9259288), this is a different nucleotide change and cannot be directly applied. Details ▾Hide ▴
Still missing
- No co-segregation data for c.253+1G>A
BS4 No segregation data are available for c.253+1G>A to assess lack of segregation in affected family members. The PTEN VCEP BS4 requires lack of segregation in one or more families. Details ▾Hide ▴
Still missing
- No segregation data available for this variant
PS5 No new data for this criterion beyond the assessment skip instruction. Details ▾Hide ▴
No further detail was recorded.
Not applicable · 8· recorded as not applicable Show reasons ▾Hide reasons ▴
PM5 N/APM5 applies to missense changes at an amino acid residue where a different pathogenic missense change has been seen. c.253+1G>A is a splice site variant, not a missense change. Details ▾Hide ▴
No further detail was recorded.
PP2 N/APP2 applies to missense variants in genes with a low rate of benign missense variation. c.253+1G>A is a canonical splice site variant, not a missense change. PTEN VCEP PP2 specification is explicit for missense variants. Details ▾Hide ▴
Sources
PP3 N/APer ClinGen SVI PVS1 recommendations (PMC6185798), PP3 should not be stacked with PVS1 for the same splice-effect prediction evidence. Additionally, the PTEN VCEP PP3 rule requires concordance of SpliceAI and VarSeak for splicing variants; VarSeak data are not available. SpliceAI max delta is 0.99, but this evidence is already captured by PVS1 for this canonical splice variant. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.99 (donor loss 0.99)
- PP3 not stackable with PVS1 per ClinGen SVI guidance
Still missing
- VarSeak score not available for PTEN VCEP concordance requirement
Sources
PP4 VCEPPTEN VCEP specifies PP4 as Not Applicable; phenotype specificity has been incorporated into the rule specifications for PS4. Details ▾Hide ▴
Sources
PP5 VCEPPTEN VCEP specifies PP5 as Not Applicable for this VCEP, per ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation. Details ▾Hide ▴
Sources
BP1 VCEPPTEN VCEP specifies BP1 as Not Applicable; this rule is not applicable to PTEN. Details ▾Hide ▴
Sources
BP6 VCEPPTEN VCEP specifies BP6 as Not Applicable for this VCEP, per ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation. Details ▾Hide ▴
Sources
BP7 N/APTEN VCEP BP7 specifies that intronic variants must be positioned at or beyond +7/-21 from the splice junction. c.253+1G>A is at the +1 position, which is the canonical splice donor site, not at or beyond +7/-21. Additionally, BP7 requires splicing prediction algorithms to predict no impact, which is contradicted by SpliceAI delta 0.99. Details ▾Hide ▴
Evidence considered
- Variant at +1 position
- not at or beyond +7/-21
- SpliceAI max delta 0.99 predicts splicing impact
Sources
Identifiers
- Gene
- PTEN
- Transcript
- NM_000314.6
- Coding (HGVS c.)
- NM_000314.6:c.253+1G>A
- Protein (HGVS p.)
- NP_000305.3:p.?
- GRCh38
- chr10:87931090 G>A
- GRCh37
- chr10:89690847 G>A
- ClinVar
- 7820, 468676
- COSMIC
- COSV64289910
Gene diagram
Every interpreted variant in PTEN, mapped onto the exon structure of NM_000314.6. Select a row to find it on the plot.
PTENNM_000314.6
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
Allele count data not recorded
gnomAD v2.1
Allele count data not recorded
gnomAD-Canada v1.0
Allele count data not recorded
Statements
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- 0.317
How the predictions were used
BP4 PTEN VCEP BP4 for splicing variants requires SpliceAI scores of 0-0.2 (evidence of benign) with VarSeak concordance. SpliceAI max delta for c.253+1G>A is 0.99, predicting a strong splicing impact, which contradicts BP4 application. Additionally, functional data (PMID:28677221) confirms splicing disruption. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.99 contradicts benign splicing prediction
- PMID:28677221 confirms exon 4 skipping and functional impact
Sources
PP3 N/APer ClinGen SVI PVS1 recommendations (PMC6185798), PP3 should not be stacked with PVS1 for the same splice-effect prediction evidence. Additionally, the PTEN VCEP PP3 rule requires concordance of SpliceAI and VarSeak for splicing variants; VarSeak data are not available. SpliceAI max delta is 0.99, but this evidence is already captured by PVS1 for this canonical splice variant. Details ▾Hide ▴
Evidence considered
- SpliceAI max delta 0.99 (donor loss 0.99)
- PP3 not stackable with PVS1 per ClinGen SVI guidance
Still missing
- VarSeak score not available for PTEN VCEP concordance requirement
Sources
BP7 N/APTEN VCEP BP7 specifies that intronic variants must be positioned at or beyond +7/-21 from the splice junction. c.253+1G>A is at the +1 position, which is the canonical splice donor site, not at or beyond +7/-21. Additionally, BP7 requires splicing prediction algorithms to predict no impact, which is contradicted by SpliceAI delta 0.99. Details ▾Hide ▴
Evidence considered
- Variant at +1 position
- not at or beyond +7/-21
- SpliceAI max delta 0.99 predicts splicing impact
Sources
Statement
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.99). BayesDel score = 0.317417.
9 paper records listed. 2 cited in the classification.
Cited in the classification
-
PMID 28677221 ↗Characterization of cryptic splicing in germline PTEN intronic variants in Cowden syndrome.Chen HJ et al. · 2017 Octc.253+1G>A was characterized in a Cowden syndrome patient. RT-PCR of patient-derived lymphoblastoid cells demonstrated exon 4 skipping resulting in frameshift p.(Ala72Thrfs*5). PTEN protein expression was significantly decreased and P-AKT was significantly increased in the group of intronic variants with splicing alterations. The variant is listed in Table 1 alongside c.253+1G>T, c.253+5G>T, and c.253+5G>A, all causing exon 4 skipping.→ PVS1 → PS1 → PS3 Names this variant
Source detail
c.253+1G>A 4 Exon 4 skipping p. (Ala72Thrfs * 5) 1
Location Table 1; Results, paragraph describing exon 4 splice mutations
Context RT-PCR from patient-derived lymphoblastoid cell lines, Western blot for PTEN/P-AKT/P-ERK1/2 protein expression
-
PMID 9259288 ↗Germline mutations in the PTEN/MMAC1 gene in patients with Cowden disease.Reports a splice site mutation at the same nucleotide position: c.253+1G>T (described as 'GT to TT, intron 4, splice site mutation') in family N4 with Cowden disease. The mutation was shown to completely cosegregate with CD in the family. c.253+1G>A was not identified in this paper.→ PS1 Does not name this variant
Source detail
In family N4 the first nucleotide of intron 4 was changed from G into T causing a mutation in the nearly invariant splice site sequence GU to UU.
Location Table 1, family N4 entry; Results, splice site mutation paragraph
Context Genomic DNA sequencing from lymphocyte DNA of CD patients
Other recorded publications
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PMID 16199547 ↗Splicing in action: assessing disease causing sequence changes.Baralle D et al. · 2005A general review of splicing mechanisms in human disease. Discusses how mutations in splicing regulatory elements can cause exon skipping, intron retention, or activation of cryptic splice sites. Does not mention PTEN or c.253+1G>A.Does not name this variant
-
PMID 20600018 ↗Frequent gastrointestinal polyps and colorectal adenocarcinomas in a prospective series of PTEN mutation carriers.Heald B et al. · 2010Lists c.253+1G>A in a table of PTEN mutation carriers undergoing prospective gastrointestinal phenotype evaluation. The patient had 'Numerous' GI polyps. The paper describes frequent GI polyps and colorectal adenocarcinomas in PTEN mutation carriers with Cowden syndrome.Names this variant
Quoted passage
139 253+1G>A Numerous
Patient data table (mutation list with polyp counts)
-
PMID 30311380 ↗Gene-specific criteria for PTEN variant curation: Recommendations from the ClinGen PTEN Expert Panel.Mester JL et al. · 2018Describes the ClinGen PTEN Expert Panel specifications to the ACMG/AMP variant interpretation guidelines. Provides the authoritative VCEP rules used in this assessment but does not mention c.253+1G>A specifically.Does not name this variant
-
PMID 9467011 ↗Mutation spectrum and genotype-phenotype analyses in Cowden disease and Bannayan-Zonana syndrome, two hamartoma syndromes with germline PTEN mutation.Reports the PTEN mutation spectrum in 37 Cowden disease and 7 Bannayan-Zonana syndrome families. Lists 30 distinct germline PTEN mutations including splice site variants IVS2-2A>G, IVS3+5G>A, and G165V (likely splice), but c.253+1G>A is not among the reported mutations. No mutations were found in exon 4 or intron 4.Does not name this variant
Quoted passage
three (10%) were splice site mutations
Table 1; Results section
-
PMID 9740666 ↗Mapping an endometrial cancer tumor suppressor gene at 10q25 and development of a bacterial clone contig for the consensus deletion interval.Maps an endometrial cancer tumor suppressor gene at 10q25 and develops a bacterial clone contig for the consensus deletion interval. Focuses on chromosomal mapping and LOH studies in endometrial cancer, not on PTEN mutation analysis. c.253+1G>A was not identified.Does not name this variant
-
PMID 17392385 ↗American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography.American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. Discusses screening recommendations for women at elevated breast cancer risk. Does not mention PTEN, c.253+1G>A, or any specific variant.Does not name this variant
-
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
Captured gnomAD v4.1 source record
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.990
Open source ↗
ClinVar
7 Pathogenic
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/7820/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/10-89690847-G-A?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr10-87931090-G-A?dataset=gn…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/10-87931090-G-A
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_000314.6%3Ac.253%…
- OncoKB ↗www.oncokb.org/gene/PTEN/?
- COSMIC ↗cancer.sanger.ac.uk/cosmic/mutation/overview?id=139182961
Statements for reports
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Pathogenic (7 clinical laboratories). (ClinVarID = 7820)
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.99). BayesDel score = 0.317417.
Somatic
This variant has previously been reported in somatic cancers (COSMIC; COSV64289910, n = 8 times).