rs10513196

Variant names:

• chr3-107506831-G-A
• rs10513196

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0450 AC: 1863 AN: 41380

American (AMR) AF: 0.192 AC: 2912 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3464

East Asian (EAS) AF: 0.116 AC: 598 AN: 5162

South Asian (SAS) AF: 0.123 AC: 590 AN: 4800

European-Finnish (FIN) AF: 0.178 AC: 1868 AN: 10486

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16062 AN: 67908

Other (OTH) AF: 0.175 AC: 370 AN: 2112

Alfa AF: 0.161 Hom.: 831

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10513196; hg19: chr3-107225678;