rs10496159

Variant names:

• chr2-68007616-G-A
• rs10496159

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 0.103 in 152,016 control chromosomes in the GnomAD database, including 2,062 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 (2062 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 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: 0.103 AC: 15577 AN: 151898 Hom.: 2052 Cov.: 31

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0388

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0115

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0162

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.103 AC: 15625 AN: 152016 Hom.: 2062 Cov.: 31 AF XY: 0.100 AC XY: 7428 AN XY: 74312

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.0388

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.0216

Gnomad4 FIN AF: 0.0115

Gnomad4 NFE AF: 0.0163

Gnomad4 OTH AF: 0.0724

Alfa AF: 0.0673 Hom.: 161

Bravo AF: 0.116

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496159; hg19: chr2-68234748;