2-63452-T-G

Variant names:

• chr2-63452-T-G
• rs957298

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 0.0872 in 152,092 control chromosomes in the GnomAD database, including 832 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 0.087 (832 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) 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: 0.0872 AC: 13249 AN: 151974 Hom.: 831 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0733

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0248

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0578

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0872 AC: 13270 AN: 152092 Hom.: 832 Cov.: 32 AF XY: 0.0842 AC XY: 6262 AN XY: 74372

African (AFR) AF: 0.172 AC: 7140 AN: 41446

American (AMR) AF: 0.0732 AC: 1119 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 390 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.0245 AC: 118 AN: 4826

European-Finnish (FIN) AF: 0.0368 AC: 390 AN: 10586

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0578 AC: 3928 AN: 67992

Other (OTH) AF: 0.0749 AC: 158 AN: 2110

Alfa AF: 0.0603 Hom.: 171

Bravo AF: 0.0940

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.52
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs957298; hg19: chr2-63452;