chr3-179528765-G-A

Variant names:

• chr3-179528765-G-A
• rs1362645
• ENST00000727849.1:n.92+3655G>A

Variant summary

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

The ENST00000727849.1(ENSG00000295079):​n.92+3655G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,150 control chromosomes in the GnomAD database, including 35,400 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 0.68 (35400 hom., cov: 32)
• Consequence: ENSG00000295079 ENST00000727849.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999
• Publications: 2 publications found

Genes affected

ENSG00000295079 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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
ENSG00000295079	ENST00000727849.1	n.92+3655G>A		intron_variant	Intron 1 of 1
ENSG00000295099	ENST00000727997.1	n.188+1372G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102808 AN: 152032 Hom.: 35341 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.676 AC: 102925 AN: 152150 Hom.: 35400 Cov.: 32 AF XY: 0.681 AC XY: 50642 AN XY: 74360

African (AFR) AF: 0.732 AC: 30376 AN: 41512

American (AMR) AF: 0.733 AC: 11213 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2409 AN: 3468

East Asian (EAS) AF: 0.984 AC: 5107 AN: 5192

South Asian (SAS) AF: 0.706 AC: 3404 AN: 4822

European-Finnish (FIN) AF: 0.689 AC: 7277 AN: 10558

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41080 AN: 67978

Other (OTH) AF: 0.687 AC: 1450 AN: 2112

Alfa AF: 0.639 Hom.: 8516

Bravo AF: 0.683

Asia WGS AF: 0.834 AC: 2896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.70
DANN	Benign	0.73
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1362645; hg19: chr3-179246553;