rs10497795

Variant names:

• chr2-196622901-C-A
• rs10497795

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 0.102 in 152,220 control chromosomes in the GnomAD database, including 842 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 (842 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 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: 0.102 AC: 15572 AN: 152102 Hom.: 841 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.0733

Gnomad EAS AF: 0.00694

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.102 AC: 15583 AN: 152220 Hom.: 842 Cov.: 32 AF XY: 0.0995 AC XY: 7408 AN XY: 74426

African (AFR) AF: 0.129 AC: 5348 AN: 41546

American (AMR) AF: 0.0832 AC: 1271 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0733 AC: 254 AN: 3466

East Asian (EAS) AF: 0.00676 AC: 35 AN: 5178

South Asian (SAS) AF: 0.0338 AC: 163 AN: 4824

European-Finnish (FIN) AF: 0.0690 AC: 731 AN: 10598

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7336 AN: 68010

Other (OTH) AF: 0.106 AC: 225 AN: 2114

Alfa AF: 0.102 Hom.: 129

Bravo AF: 0.105

Asia WGS AF: 0.0270 AC: 94 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs10497795; hg19: chr2-197487625;