rs287474

Variant names:

• chr13-68701828-T-A
• rs287474

Your query was ambiguous. Multiple possible variants found:

• chr13-68701828-T-A
• chr13-68701828-T-C
• chr13-68701828-T-G

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 0.584 in 151,874 control chromosomes in the GnomAD database, including 26,132 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 0.58 (26132 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88649 AN: 151758 Hom.: 26101 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.584 AC: 88723 AN: 151874 Hom.: 26132 Cov.: 32 AF XY: 0.587 AC XY: 43550 AN XY: 74234

African (AFR) AF: 0.520 AC: 21547 AN: 41400

American (AMR) AF: 0.666 AC: 10164 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2006 AN: 3468

East Asian (EAS) AF: 0.687 AC: 3546 AN: 5158

South Asian (SAS) AF: 0.591 AC: 2845 AN: 4814

European-Finnish (FIN) AF: 0.643 AC: 6763 AN: 10514

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39791 AN: 67940

Other (OTH) AF: 0.583 AC: 1229 AN: 2108

Alfa AF: 0.487 Hom.: 1489

Bravo AF: 0.582

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.16
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs287474; hg19: chr13-69275960;