rs8032019

Variant names:

• chr15-34699289-A-G
• rs8032019
• ENST00000720751.1:n.234+21028T>C

Variant summary

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

The ENST00000720751.1(ENSG00000294065):​n.234+21028T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,822 control chromosomes in the GnomAD database, including 8,885 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 0.34 (8885 hom., cov: 31)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 9 publications found

Genes affected

ENSG00000294065 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 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
ENSG00000294065	ENST00000720751.1	n.234+21028T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51753 AN: 151704 Hom.: 8875 Cov.: 31

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.341 AC: 51783 AN: 151822 Hom.: 8885 Cov.: 31 AF XY: 0.339 AC XY: 25177 AN XY: 74222

African (AFR) AF: 0.336 AC: 13891 AN: 41302

American (AMR) AF: 0.297 AC: 4538 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3472

East Asian (EAS) AF: 0.396 AC: 2039 AN: 5148

South Asian (SAS) AF: 0.406 AC: 1954 AN: 4808

European-Finnish (FIN) AF: 0.292 AC: 3085 AN: 10574

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24109 AN: 67936

Other (OTH) AF: 0.329 AC: 693 AN: 2104

Alfa AF: 0.337 Hom.: 5166

Bravo AF: 0.340

Asia WGS AF: 0.415 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.78
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs8032019; hg19: chr15-34991490;