chr2-81441684-T-C

Variant names:

• chr2-81441684-T-C
• rs10496265

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;