rs10496265

Positions:

• chr2-81441684-T-C

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 0.118 in 151,218 control chromosomes in the GnomAD database, including 1,351 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 (1351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17797 AN: 151100 Hom.: 1351 Cov.: 32

Gnomad AFR AF: 0.0427

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.0816

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00918

Gnomad SAS AF: 0.0464

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.118 AC: 17795 AN: 151218 Hom.: 1351 Cov.: 32 AF XY: 0.114 AC XY: 8449 AN XY: 73882

Gnomad4 AFR AF: 0.0426

Gnomad4 AMR AF: 0.0815

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.00920

Gnomad4 SAS AF: 0.0465

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.100

Alfa AF: 0.149 Hom.: 1253

Bravo AF: 0.108

Asia WGS AF: 0.0250 AC: 87 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496265; hg19: chr2-81668808;