rs4686428

Variant names:

• chr3-186529584-G-A
• rs4686428

Your query was ambiguous. Multiple possible variants found:

• chr3-186529584-G-A
• chr3-186529584-G-C

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 0.811 in 152,100 control chromosomes in the GnomAD database, including 50,230 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 0.81 (50230 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 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: 0.811 AC: 123253 AN: 151982 Hom.: 50175 Cov.: 31

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.811 AC: 123367 AN: 152100 Hom.: 50230 Cov.: 31 AF XY: 0.814 AC XY: 60511 AN XY: 74348

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.839

Alfa AF: 0.786 Hom.: 95007

Bravo AF: 0.821

Asia WGS AF: 0.866 AC: 3011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4686428; hg19: chr3-186247373;