rs10513598

Positions:

• chr3-162986232-G-A
• chr3-162986232-G-C
• chr3-162986232-G-T

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 0.0998 in 152,106 control chromosomes in the GnomAD database, including 792 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 0.10 (792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

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 (NFE) allele frequency at 95% confidence interval = 0.105 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: 0.100 AC: 15193 AN: 151988 Hom.: 792 Cov.: 32

Gnomad AFR AF: 0.0988

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0939

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.0998 AC: 15186 AN: 152106 Hom.: 792 Cov.: 32 AF XY: 0.0982 AC XY: 7303 AN XY: 74342

Gnomad4 AFR AF: 0.0985

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0939

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0792

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.121

Alfa AF: 0.101 Hom.: 560

Bravo AF: 0.0980

Asia WGS AF: 0.0470 AC: 163 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	5.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513598; hg19: chr3-162704020;