7-5987397-A-G

Variant names:

• chr7-5987397-A-G
• rs587780723
• NM_000535.7:c.1368T>C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6_Very_Strong BP7

The NM_000535.7(PMS2):​c.1368T>C​(p.Ser456Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,614,070 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000075 (0 hom.)
• Consequence: PMS2 NM_000535.7 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9
• Conservation: PhyloP100: -0.475
• Publications: 0 publications found

Genes affected

PMS2 (HGNC:9122): (PMS1 homolog 2, mismatch repair system component) The protein encoded by this gene is a key component of the mismatch repair system that functions to correct DNA mismatches and small insertions and deletions that can occur during DNA replication and homologous recombination. This protein forms heterodimers with the gene product of the mutL homolog 1 (MLH1) gene to form the MutL-alpha heterodimer. The MutL-alpha heterodimer possesses an endonucleolytic activity that is activated following recognition of mismatches and insertion/deletion loops by the MutS-alpha and MutS-beta heterodimers, and is necessary for removal of the mismatched DNA. There is a DQHA(X)2E(X)4E motif found at the C-terminus of the protein encoded by this gene that forms part of the active site of the nuclease. Mutations in this gene have been associated with hereditary nonpolyposis colorectal cancer (HNPCC; also known as Lynch syndrome) and Turcot syndrome. [provided by RefSeq, Apr 2016]

PMS2 Gene-Disease associations (from GenCC):

• Lynch syndrome

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
• Lynch syndrome 4

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• mismatch repair cancer syndrome 1

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
• mismatch repair cancer syndrome 4

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• malignant pancreatic neoplasm

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• ovarian cancer

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• Muir-Torre syndrome

  Inheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
• rhabdomyosarcoma

  Inheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
• breast cancer

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• prostate cancer

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• hereditary breast carcinoma

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 7-5987397-A-G is Benign according to our data. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5987397-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 135935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.475 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PMS2	NM_000535.7	c.1368T>C	p.Ser456Ser	synonymous_variant	Exon 11 of 15	ENST00000265849.12	NP_000526.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PMS2	ENST00000265849.12	c.1368T>C	p.Ser456Ser	synonymous_variant	Exon 11 of 15	1	NM_000535.7	ENSP00000265849.7

Frequencies

GnomAD3 genomes AF: 0.0000131 AC: 2 AN: 152184 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000752 AC: 11 AN: 1461886 Hom.: 0 Cov.: 34 AF XY: 0.0000110 AC XY: 8 AN XY: 727246

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.000101 AC: 4 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53418

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000629 AC: 7 AN: 1112006

Other (OTH) AF: 0.00 AC: 0 AN: 60396

GnomAD4 genome AF: 0.0000131 AC: 2 AN: 152184 Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1 AN XY: 74350

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 41438

American (AMR) AF: 0.00 AC: 0 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5196

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10626

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 68032

Other (OTH) AF: 0.00 AC: 0 AN: 2092

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.029673), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0000267 Hom.: 0

Bravo AF: 0.0000113

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Jun 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PMS2: BP4, BP7 -

May 08, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Benign:2

Mar 29, 2018

Color Diagnostics, LLC DBA Color Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 15, 2015

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

not specified Benign:1

Aug 03, 2020

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breast and/or ovarian cancer Benign:1

Dec 07, 2021

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Lynch syndrome Benign:1

Feb 05, 2024

All of Us Research Program, National Institutes of Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary nonpolyposis colorectal neoplasms Benign:1

Dec 13, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Lynch syndrome 4 Benign:1

Jan 30, 2025

Myriad Genetics, Inc.

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.14
DANN	Benign	0.51
PhyloP100		-0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs587780723; hg19: chr7-6027028;