2-47463272-T-C

Variant names:

• chr2-47463272-T-C
• rs3771280
• NM_000251.3:c.1510+118T>C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000251.3(MSH2):​c.1510+118T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 1,231,666 control chromosomes in the GnomAD database, including 84,906 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.46 (18402 hom., cov: 32)
  • Exomes 𝑓: 0.33 (66504 hom.)
• Consequence: MSH2 NM_000251.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.573

Genes affected

MSH2 (HGNC:7325): (mutS homolog 2) This locus is frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). When cloned, it was discovered to be a human homolog of the E. coli mismatch repair gene mutS, consistent with the characteristic alterations in microsatellite sequences (RER+ phenotype) found in HNPCC. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 2-47463272-T-C is Benign according to our data. Variant chr2-47463272-T-C is described in ClinVar as [Benign]. Clinvar id is 676474.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSH2	NM_000251.3	c.1510+118T>C		intron_variant	Intron 9 of 15	ENST00000233146.7	NP_000242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSH2	ENST00000233146.7	c.1510+118T>C		intron_variant	Intron 9 of 15	1	NM_000251.3	ENSP00000233146.2

Frequencies

GnomAD3 genomes AF: 0.455 AC: 68897 AN: 151428 Hom.: 18356 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.413

GnomAD4 exome AF: 0.334 AC: 360352 AN: 1080118 Hom.: 66504 AF XY: 0.332 AC XY: 182426 AN XY: 549868

Gnomad4 AFR exome AF: 0.755

Gnomad4 AMR exome AF: 0.331

Gnomad4 ASJ exome AF: 0.251

Gnomad4 EAS exome AF: 0.607

Gnomad4 SAS exome AF: 0.334

Gnomad4 FIN exome AF: 0.447

Gnomad4 NFE exome AF: 0.301

Gnomad4 OTH exome AF: 0.370

GnomAD4 genome AF: 0.455 AC: 68999 AN: 151548 Hom.: 18402 Cov.: 32 AF XY: 0.457 AC XY: 33845 AN XY: 74044

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.411

Alfa AF: 0.402 Hom.: 2316

Bravo AF: 0.463

Asia WGS AF: 0.514 AC: 1787 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 20, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.53

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

Other links and lift over

dbSNP: rs3771280; hg19: chr2-47690411;