rs10513584

Variant names:

• chr3-162522875-A-C
• rs10513584

Your query was ambiguous. Multiple possible variants found:

• chr3-162522875-A-C
• chr3-162522875-A-G
• chr3-162522875-A-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 0.16 in 152,076 control chromosomes in the GnomAD database, including 2,455 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 0.16 (2455 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06

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 (EAS) allele frequency at 95% confidence interval = 0.484 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: 0.160 AC: 24290 AN: 151958 Hom.: 2445 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.160 AC: 24307 AN: 152076 Hom.: 2455 Cov.: 32 AF XY: 0.166 AC XY: 12327 AN XY: 74340

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.168

Alfa AF: 0.144 Hom.: 221

Bravo AF: 0.155

Asia WGS AF: 0.400 AC: 1382 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.5
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513584; hg19: chr3-162240663;