2-2515741-C-T

Variant names:

• chr2-2515741-C-T
• rs10199521

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.227 in 151,984 control chromosomes in the GnomAD database, including 3,973 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 0.23 (3973 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 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: 0.227 AC: 34468 AN: 151866 Hom.: 3963 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.227 AC: 34518 AN: 151984 Hom.: 3973 Cov.: 32 AF XY: 0.225 AC XY: 16697 AN XY: 74288

African (AFR) AF: 0.274 AC: 11368 AN: 41418

American (AMR) AF: 0.180 AC: 2748 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3466

East Asian (EAS) AF: 0.329 AC: 1692 AN: 5150

South Asian (SAS) AF: 0.261 AC: 1258 AN: 4814

European-Finnish (FIN) AF: 0.169 AC: 1785 AN: 10576

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14285 AN: 67972

Other (OTH) AF: 0.216 AC: 457 AN: 2116

Alfa AF: 0.216 Hom.: 12943

Bravo AF: 0.230

Asia WGS AF: 0.286 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.036
DANN	Benign	0.53
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10199521; hg19: chr2-2519513;