rs7176681

Variant names:

• chr15-79635202-C-T
• rs7176681
• ENST00000756109.1:n.209-26770G>A

Variant summary

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

The ENST00000756109.1(ENSG00000298511):​n.209-26770G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,058 control chromosomes in the GnomAD database, including 4,106 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 0.23 (4106 hom., cov: 32)
• Consequence: ENSG00000298511 ENST00000756109.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 4 publications found

Genes affected

ENSG00000298511 (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 (NFE) allele frequency at 95% confidence interval = 0.254 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
ENSG00000298511	ENST00000756109.1	n.209-26770G>A		intron_variant	Intron 3 of 3
ENSG00000298511	ENST00000756110.1	n.168-26770G>A		intron_variant	Intron 2 of 2
ENSG00000298511	ENST00000756111.1	n.319+26690G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35037 AN: 151940 Hom.: 4107 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.231 AC: 35064 AN: 152058 Hom.: 4106 Cov.: 32 AF XY: 0.226 AC XY: 16788 AN XY: 74322

African (AFR) AF: 0.220 AC: 9118 AN: 41478

American (AMR) AF: 0.182 AC: 2789 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3466

East Asian (EAS) AF: 0.146 AC: 756 AN: 5172

South Asian (SAS) AF: 0.240 AC: 1151 AN: 4804

European-Finnish (FIN) AF: 0.180 AC: 1905 AN: 10568

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17496 AN: 67966

Other (OTH) AF: 0.214 AC: 451 AN: 2112

Alfa AF: 0.239 Hom.: 546

Bravo AF: 0.228

Asia WGS AF: 0.207 AC: 718 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	0.024
DANN	Benign	0.53
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7176681; hg19: chr15-79927544;