rs4894332

Variant names:

• chr3-138931900-A-C
• rs4894332

Your query was ambiguous. Multiple possible variants found:

• chr3-138931900-A-C
• chr3-138931900-A-G
• chr3-138931900-A-T

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 0.223 in 152,212 control chromosomes in the GnomAD database, including 5,918 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 0.22 (5918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33841 AN: 152094 Hom.: 5890 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.223 AC: 33923 AN: 152212 Hom.: 5918 Cov.: 32 AF XY: 0.230 AC XY: 17124 AN XY: 74424

African (AFR) AF: 0.415 AC: 17198 AN: 41490

American (AMR) AF: 0.278 AC: 4243 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 411 AN: 3472

East Asian (EAS) AF: 0.631 AC: 3266 AN: 5180

South Asian (SAS) AF: 0.149 AC: 719 AN: 4832

European-Finnish (FIN) AF: 0.196 AC: 2084 AN: 10608

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0802 AC: 5455 AN: 68026

Other (OTH) AF: 0.207 AC: 438 AN: 2114

Alfa AF: 0.170 Hom.: 616

Bravo AF: 0.244

Asia WGS AF: 0.414 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.9
DANN	Benign	0.78
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs4894332; hg19: chr3-138650742;