rs10497297

Variant names:

• chr2-166680707-G-A
• rs10497297

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 0.627 in 150,894 control chromosomes in the GnomAD database, including 31,639 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 0.63 (31639 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.744 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: 0.628 AC: 94616 AN: 150780 Hom.: 31633 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.667

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.627 AC: 94640 AN: 150894 Hom.: 31639 Cov.: 32 AF XY: 0.627 AC XY: 46167 AN XY: 73652

African (AFR) AF: 0.372 AC: 15263 AN: 41018

American (AMR) AF: 0.728 AC: 11056 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2219 AN: 3448

East Asian (EAS) AF: 0.572 AC: 2923 AN: 5114

South Asian (SAS) AF: 0.564 AC: 2581 AN: 4578

European-Finnish (FIN) AF: 0.728 AC: 7629 AN: 10476

Middle Eastern (MID) AF: 0.666 AC: 193 AN: 290

European-Non Finnish (NFE) AF: 0.749 AC: 50782 AN: 67774

Other (OTH) AF: 0.637 AC: 1338 AN: 2100

Alfa AF: 0.665 Hom.: 4548

Bravo AF: 0.616

Asia WGS AF: 0.546 AC: 1888 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.36
DANN	Benign	0.52
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs10497297; hg19: chr2-167537217;