rs7163001

Variant names:

• chr15-34698373-G-A
• rs7163001
• ENST00000720751.1:n.234+21944C>T

Variant summary

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

The ENST00000720751.1(ENSG00000294065):​n.234+21944C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,756 control chromosomes in the GnomAD database, including 12,777 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 0.41 (12777 hom., cov: 32)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 7 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 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+21944C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61904 AN: 151640 Hom.: 12773 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.408 AC: 61939 AN: 151756 Hom.: 12777 Cov.: 32 AF XY: 0.407 AC XY: 30147 AN XY: 74120

African (AFR) AF: 0.377 AC: 15596 AN: 41340

American (AMR) AF: 0.373 AC: 5685 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1196 AN: 3470

East Asian (EAS) AF: 0.438 AC: 2250 AN: 5140

South Asian (SAS) AF: 0.587 AC: 2816 AN: 4798

European-Finnish (FIN) AF: 0.348 AC: 3658 AN: 10504

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29199 AN: 67952

Other (OTH) AF: 0.408 AC: 860 AN: 2106

Alfa AF: 0.403 Hom.: 1616

Bravo AF: 0.404

Asia WGS AF: 0.514 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.063
DANN	Benign	0.69
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs7163001; hg19: chr15-34990574;