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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.584 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

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.583

Alfa AF: 0.487 Hom.: 1489

Bravo AF: 0.582

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs287474; hg19: chr13-69275960;