rs4686428

Variant names:

• chr3-186529584-G-A
• rs4686428
• ENST00000727128.1:n.187+7764G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000727128.1(ENSG00000294974):​n.187+7764G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000294974 ENST00000727128.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 6 publications found

Genes affected

ENSG00000294974 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000294974	ENST00000727128.1	n.187+7764G>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.863 AC: 35794 AN: 41492

American (AMR) AF: 0.853 AC: 13050 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2966 AN: 3470

East Asian (EAS) AF: 0.899 AC: 4659 AN: 5180

South Asian (SAS) AF: 0.862 AC: 4149 AN: 4812

European-Finnish (FIN) AF: 0.742 AC: 7843 AN: 10570

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52295 AN: 67982

Other (OTH) AF: 0.839 AC: 1761 AN: 2100

Alfa AF: 0.792 Hom.: 152065

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4686428; hg19: chr3-186247373;