rs3928291

Variant names:

• chr9-129414472-G-A
• rs3928291
• ENST00000726583.1:n.578G>A

Variant summary

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

The ENST00000726583.1(ENSG00000294888):​n.578G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,174 control chromosomes in the GnomAD database, including 1,954 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 0.14 (1954 hom., cov: 32)
• Consequence: ENSG00000294888 ENST00000726583.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 6 publications found

Genes affected

ENSG00000294888 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 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
ENSG00000294888	ENST00000726583.1	n.578G>A		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000294888	ENST00000726582.1	n.223+728G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21206 AN: 152056 Hom.: 1956 Cov.: 32

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.139 AC: 21198 AN: 152174 Hom.: 1954 Cov.: 32 AF XY: 0.141 AC XY: 10501 AN XY: 74382

African (AFR) AF: 0.0357 AC: 1485 AN: 41540

American (AMR) AF: 0.149 AC: 2272 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 564 AN: 3470

East Asian (EAS) AF: 0.166 AC: 862 AN: 5178

South Asian (SAS) AF: 0.318 AC: 1531 AN: 4816

European-Finnish (FIN) AF: 0.146 AC: 1544 AN: 10570

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12531 AN: 67988

Other (OTH) AF: 0.135 AC: 284 AN: 2108

Alfa AF: 0.171 Hom.: 4703

Bravo AF: 0.130

Asia WGS AF: 0.195 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.9
DANN	Benign	0.83
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs3928291; hg19: chr9-132176751; COSMIC: COSV60402868;