13-75935398-A-G

Variant names:

• chr13-75935398-A-G
• rs1340713

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.585 in 151,984 control chromosomes in the GnomAD database, including 26,292 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (26292 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88862 AN: 151866 Hom.: 26256 Cov.: 33

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.585 AC: 88959 AN: 151984 Hom.: 26292 Cov.: 33 AF XY: 0.586 AC XY: 43510 AN XY: 74270

African (AFR) AF: 0.526 AC: 21807 AN: 41464

American (AMR) AF: 0.632 AC: 9659 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1691 AN: 3464

East Asian (EAS) AF: 0.638 AC: 3292 AN: 5158

South Asian (SAS) AF: 0.547 AC: 2635 AN: 4816

European-Finnish (FIN) AF: 0.618 AC: 6532 AN: 10564

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.611 AC: 41536 AN: 67936

Other (OTH) AF: 0.564 AC: 1187 AN: 2104

Alfa AF: 0.597 Hom.: 9066

Bravo AF: 0.584

Asia WGS AF: 0.621 AC: 2155 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1340713; hg19: chr13-76509534; COSMIC: COSV73841979;