rs2063640

Variant names:

• chr3-102484201-C-A
• rs2063640

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 0.101 in 152,218 control chromosomes in the GnomAD database, including 1,114 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 0.10 (1114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 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: 0.101 AC: 15304 AN: 152098 Hom.: 1109 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0975

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.101 AC: 15318 AN: 152218 Hom.: 1114 Cov.: 32 AF XY: 0.104 AC XY: 7726 AN XY: 74404

Gnomad4 AFR AF: 0.0434

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.0885

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.0875

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.0976

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0990 Hom.: 1031

Bravo AF: 0.105

Asia WGS AF: 0.170 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2063640; hg19: chr3-102203045;