rs2063640

Variant names:

• chr3-102484201-C-A
• rs2063640

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 0.101 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
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0434 AC: 1802 AN: 41556

American (AMR) AF: 0.209 AC: 3204 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0885 AC: 307 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1337 AN: 5162

South Asian (SAS) AF: 0.0875 AC: 421 AN: 4810

European-Finnish (FIN) AF: 0.121 AC: 1287 AN: 10594

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0976 AC: 6636 AN: 68010

Other (OTH) AF: 0.113 AC: 238 AN: 2110

Alfa AF: 0.101 Hom.: 1529

Bravo AF: 0.105

Asia WGS AF: 0.170 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.7
DANN	Benign	0.40
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2063640; hg19: chr3-102203045;