rs10497837

Variant names:

• chr2-199592620-C-T
• rs10497837

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 0.126 in 152,112 control chromosomes in the GnomAD database, including 1,572 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 0.13 (1572 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 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: 0.126 AC: 19135 AN: 151994 Hom.: 1571 Cov.: 32

Gnomad AFR AF: 0.0501

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0240

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.126 AC: 19132 AN: 152112 Hom.: 1572 Cov.: 32 AF XY: 0.123 AC XY: 9178 AN XY: 74344

African (AFR) AF: 0.0501 AC: 2078 AN: 41518

American (AMR) AF: 0.111 AC: 1692 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3472

East Asian (EAS) AF: 0.0242 AC: 125 AN: 5160

South Asian (SAS) AF: 0.205 AC: 988 AN: 4816

European-Finnish (FIN) AF: 0.107 AC: 1134 AN: 10592

Middle Eastern (MID) AF: 0.238 AC: 69 AN: 290

European-Non Finnish (NFE) AF: 0.174 AC: 11827 AN: 67974

Other (OTH) AF: 0.137 AC: 289 AN: 2110

Alfa AF: 0.166 Hom.: 1376

Bravo AF: 0.121

Asia WGS AF: 0.0960 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0090
DANN	Benign	0.68
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10497837; hg19: chr2-200457343;