rs10497837

chr2-199592620-C-T

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 0.126 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0501

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.0242

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.137

Alfa AF: 0.166 Hom.: 1274

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497837; hg19: chr2-200457343;