rs5742910

Positions:

• chr13-113105516-T-TTCCTATATCC

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 29, 2022

See Variant Classification Assertion Criteria. -

Myocardial infarction, decreased susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Sep 14, 2000

- -

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;