3-10733074-C-T

Variant names:

• chr3-10733074-C-T
• rs1682825
• ENST00000827165.1:n.391+5592G>A

Variant summary

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

The ENST00000827165.1(ENSG00000307569):​n.391+5592G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 151,954 control chromosomes in the GnomAD database, including 51,760 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 0.82 (51760 hom., cov: 31)
• Consequence: ENSG00000307569 ENST00000827165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 4 publications found

Genes affected

ENSG00000307569 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 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
ENSG00000307569	ENST00000827165.1	n.391+5592G>A		intron_variant	Intron 1 of 1
ENSG00000307569	ENST00000827166.1	n.338+5592G>A		intron_variant	Intron 1 of 2
ENSG00000307569	ENST00000827167.1	n.338+5592G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125095 AN: 151836 Hom.: 51710 Cov.: 31

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.824 AC: 125201 AN: 151954 Hom.: 51760 Cov.: 31 AF XY: 0.823 AC XY: 61115 AN XY: 74270

African (AFR) AF: 0.871 AC: 36126 AN: 41468

American (AMR) AF: 0.807 AC: 12251 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2981 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3252 AN: 5156

South Asian (SAS) AF: 0.774 AC: 3731 AN: 4822

European-Finnish (FIN) AF: 0.836 AC: 8824 AN: 10560

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55419 AN: 67986

Other (OTH) AF: 0.808 AC: 1698 AN: 2102

Alfa AF: 0.814 Hom.: 211983

Bravo AF: 0.822

Asia WGS AF: 0.687 AC: 2395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.45
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs1682825; hg19: chr3-10774759;