2-63452-T-G

Position:

• chr2-63452-T-G

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 0.0872 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

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 (AFR) allele frequency at 95% confidence interval = 0.169 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: 0.0872 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

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0732

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0245

Gnomad4 FIN AF: 0.0368

Gnomad4 NFE AF: 0.0578

Gnomad4 OTH AF: 0.0749

Alfa AF: 0.0498 Hom.: 73

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs957298; hg19: chr2-63452;