rs5742910

Variant names:

• chr13-113105516-T-TTCCTATATCC
• rs5742910

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The variant allele was found at a frequency of 0.175 in 152,174 control chromosomes in the GnomAD database, including 2,907 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (2907 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1 O:1
• Conservation: PhyloP100: -0.243

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 13-113105516-T-TTCCTATATCC is Benign according to our data. Variant chr13-113105516-T-TTCCTATATCC is described in ClinVar as [Benign]. Clinvar id is 12079.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26632 AN: 152056 Hom.: 2899 Cov.: 28

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0397

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.181

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.175 AC: 26673 AN: 152174 Hom.: 2907 Cov.: 28 AF XY: 0.174 AC XY: 12964 AN XY: 74422

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0398

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.0759

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.180

Alfa AF: 0.0523 Hom.: 54

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 29, 2022

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

See Variant Classification Assertion Criteria. -

Myocardial infarction, decreased susceptibility to Other:1

Sep 14, 2000

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5742910; hg19: chr13-113759830;