rs10497997

Variant names:

• chr2-213239055-C-T
• rs10497997

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 0.0215 in 152,290 control chromosomes in the GnomAD database, including 43 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 0.021 (43 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0516 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: 0.0215 AC: 3276 AN: 152172 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.00581

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0195

Gnomad ASJ AF: 0.0570

Gnomad EAS AF: 0.0233

Gnomad SAS AF: 0.0575

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0264

Gnomad OTH AF: 0.0288

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

GnomAD4 genome AF: 0.0215 AC: 3274 AN: 152290 Hom.: 43 Cov.: 32 AF XY: 0.0221 AC XY: 1643 AN XY: 74464

Gnomad4 AFR AF: 0.00580

Gnomad4 AMR AF: 0.0197

Gnomad4 ASJ AF: 0.0570

Gnomad4 EAS AF: 0.0228

Gnomad4 SAS AF: 0.0571

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.0264

Gnomad4 OTH AF: 0.0285

Alfa AF: 0.0214 Hom.: 9

Bravo AF: 0.0200

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	17
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497997; hg19: chr2-214103779;