rs7176510

Variant names:

• chr15-34707278-C-T
• rs7176510
• ENST00000720751.1:n.234+13039G>A

Variant summary

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

The ENST00000720751.1(ENSG00000294065):​n.234+13039G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,046 control chromosomes in the GnomAD database, including 13,322 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 0.42 (13322 hom., cov: 33)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 8 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720751.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294065	ENST00000720751.1		n.234+13039G>A		intron	N/A
	ENSG00000294065	ENST00000720752.1		n.188-3736G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63227 AN: 151926 Hom.: 13315 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.416 AC: 63270 AN: 152046 Hom.: 13322 Cov.: 33 AF XY: 0.414 AC XY: 30781 AN XY: 74306

African (AFR) AF: 0.406 AC: 16846 AN: 41458

American (AMR) AF: 0.374 AC: 5718 AN: 15296

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

East Asian (EAS) AF: 0.437 AC: 2261 AN: 5176

South Asian (SAS) AF: 0.587 AC: 2829 AN: 4818

European-Finnish (FIN) AF: 0.348 AC: 3670 AN: 10546

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.430 AC: 29211 AN: 67972

Other (OTH) AF: 0.408 AC: 860 AN: 2108

Alfa AF: 0.408 Hom.: 2189

Bravo AF: 0.414

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.2
DANN	Benign	0.65
PhyloP100		0.078

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7176510;

hg19: chr15-34999479;