rs10496159

chr2-68007616-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;