rs10513196

Variant names:

• chr3-107506831-G-A
• rs10513196

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 0.165 in 151,682 control chromosomes in the GnomAD database, including 2,657 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 0.17 (2657 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.165 AC: 25081 AN: 151564 Hom.: 2660 Cov.: 31

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.165 AC: 25083 AN: 151682 Hom.: 2657 Cov.: 31 AF XY: 0.162 AC XY: 12018 AN XY: 74078

Gnomad4 AFR AF: 0.0450

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.175

Alfa AF: 0.197 Hom.: 808

Bravo AF: 0.162

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513196; hg19: chr3-107225678;