rs3815383

Positions:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000265849.12(PMS2):​c.903+84C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0738 in 836,554 control chromosomes in the GnomAD database, including 4,767 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.057 ( 573 hom., cov: 32)
Exomes 𝑓: 0.078 ( 4194 hom. )

Consequence

PMS2
ENST00000265849.12 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0480
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 7-5995450-G-A is Benign according to our data. Variant chr7-5995450-G-A is described in ClinVar as [Benign]. Clinvar id is 596289.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5995450-G-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PMS2NM_000535.7 linkuse as main transcriptc.903+84C>T intron_variant ENST00000265849.12 NP_000526.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PMS2ENST00000265849.12 linkuse as main transcriptc.903+84C>T intron_variant 1 NM_000535.7 ENSP00000265849 P3P54278-1

Frequencies

GnomAD3 genomes
AF:
0.0565
AC:
8597
AN:
152112
Hom.:
572
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0211
Gnomad AMI
AF:
0.00219
Gnomad AMR
AF:
0.0623
Gnomad ASJ
AF:
0.0628
Gnomad EAS
AF:
0.348
Gnomad SAS
AF:
0.159
Gnomad FIN
AF:
0.0942
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.0418
Gnomad OTH
AF:
0.0531
GnomAD4 exome
AF:
0.0777
AC:
53171
AN:
684324
Hom.:
4194
AF XY:
0.0803
AC XY:
29563
AN XY:
368242
show subpopulations
Gnomad4 AFR exome
AF:
0.0189
Gnomad4 AMR exome
AF:
0.0859
Gnomad4 ASJ exome
AF:
0.0654
Gnomad4 EAS exome
AF:
0.362
Gnomad4 SAS exome
AF:
0.148
Gnomad4 FIN exome
AF:
0.0934
Gnomad4 NFE exome
AF:
0.0430
Gnomad4 OTH exome
AF:
0.0731
GnomAD4 genome
AF:
0.0565
AC:
8601
AN:
152230
Hom.:
573
Cov.:
32
AF XY:
0.0613
AC XY:
4566
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.0211
Gnomad4 AMR
AF:
0.0621
Gnomad4 ASJ
AF:
0.0628
Gnomad4 EAS
AF:
0.348
Gnomad4 SAS
AF:
0.159
Gnomad4 FIN
AF:
0.0942
Gnomad4 NFE
AF:
0.0418
Gnomad4 OTH
AF:
0.0591
Alfa
AF:
0.0464
Hom.:
31
Bravo
AF:
0.0521
Asia WGS
AF:
0.244
AC:
845
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Mar 19, 2018- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMar 03, 2015This variant is associated with the following publications: (PMID: 28874130) -
Hereditary nonpolyposis colorectal neoplasms Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 15, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
1.1
DANN
Benign
0.80
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3815383; hg19: chr7-6035081; COSMIC: COSV56220430; API