rs10513582

Variant names:

• chr3-162253447-A-T
• rs10513582

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 0.0568 in 151,834 control chromosomes in the GnomAD database, including 361 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 0.057 (361 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.121 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: 0.0567 AC: 8603 AN: 151716 Hom.: 360 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0351

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.0691

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0226

Gnomad OTH AF: 0.0480

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

GnomAD4 genome AF: 0.0568 AC: 8617 AN: 151834 Hom.: 361 Cov.: 32 AF XY: 0.0587 AC XY: 4356 AN XY: 74234

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0351

Gnomad4 ASJ AF: 0.00865

Gnomad4 EAS AF: 0.0690

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0226

Gnomad4 OTH AF: 0.0475

Alfa AF: 0.0418 Hom.: 31

Bravo AF: 0.0586

Asia WGS AF: 0.0720 AC: 249 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.4
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513582; hg19: chr3-161971235;