rs10497895

chr2-208062569-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 0.115 in 151,874 control chromosomes in the GnomAD database, including 1,101 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 0.12 (1101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 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: 0.116 AC: 17532 AN: 151756 Hom.: 1101 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0364

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.115 AC: 17538 AN: 151874 Hom.: 1101 Cov.: 32 AF XY: 0.114 AC XY: 8436 AN XY: 74208

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0374

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.119

Alfa AF: 0.127 Hom.: 288

Bravo AF: 0.117

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	0.95
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497895; hg19: chr2-208927293;