13-102584853-G-A

Position:

• chr13-102584853-G-A

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 0.638 in 152,070 control chromosomes in the GnomAD database, including 32,180 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 0.64 (32180 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 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: 0.638 AC: 96911 AN: 151952 Hom.: 32142 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.638 AC: 97004 AN: 152070 Hom.: 32180 Cov.: 32 AF XY: 0.634 AC XY: 47105 AN XY: 74308

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.631

Alfa AF: 0.584 Hom.: 3164

Bravo AF: 0.650

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.94
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1887353; hg19: chr13-103237203;