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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.223 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

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.0802

Gnomad4 OTH AF: 0.207

Alfa AF: 0.162 Hom.: 548

Bravo AF: 0.244

Asia WGS AF: 0.414 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4894332; hg19: chr3-138650742;