rs10497183

Variant names:

• chr2-157359991-G-A
• rs10497183

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 0.018 in 151,474 control chromosomes in the GnomAD database, including 91 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 0.018 (91 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710
• Publications: 0 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 (AMR) allele frequency at 95% confidence interval = 0.0813 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: 0.0180 AC: 2724 AN: 151356 Hom.: 92 Cov.: 32

Gnomad AFR AF: 0.00370

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0854

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.0619

Gnomad SAS AF: 0.0401

Gnomad FIN AF: 0.0109

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00749

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0180 AC: 2721 AN: 151474 Hom.: 91 Cov.: 32 AF XY: 0.0204 AC XY: 1506 AN XY: 73970

African (AFR) AF: 0.00369 AC: 152 AN: 41188

American (AMR) AF: 0.0851 AC: 1295 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.00606 AC: 21 AN: 3468

East Asian (EAS) AF: 0.0621 AC: 320 AN: 5156

South Asian (SAS) AF: 0.0403 AC: 193 AN: 4790

European-Finnish (FIN) AF: 0.0109 AC: 114 AN: 10438

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00749 AC: 509 AN: 67914

Other (OTH) AF: 0.0181 AC: 38 AN: 2102

Alfa AF: 0.0127 Hom.: 21

Bravo AF: 0.0224

Asia WGS AF: 0.0480 AC: 169 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	0.17
DANN	Benign	0.65
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs10497183; hg19: chr2-158216503;