rs7176005

Variant names:

• chr15-51339082-C-T
• rs7176005

Variant summary

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

The variant allele was found at a frequency of 0.211 in 152,140 control chromosomes in the GnomAD database, including 4,793 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 0.21 (4793 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32071 AN: 152020 Hom.: 4777 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.0637

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.211 AC: 32141 AN: 152140 Hom.: 4793 Cov.: 32 AF XY: 0.211 AC XY: 15663 AN XY: 74378

African (AFR) AF: 0.420 AC: 17427 AN: 41446

American (AMR) AF: 0.173 AC: 2652 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 484 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1074 AN: 5172

South Asian (SAS) AF: 0.259 AC: 1250 AN: 4824

European-Finnish (FIN) AF: 0.0637 AC: 675 AN: 10604

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8001 AN: 68010

Other (OTH) AF: 0.202 AC: 427 AN: 2116

Alfa AF: 0.160 Hom.: 5169

Bravo AF: 0.227

Asia WGS AF: 0.290 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.2
DANN	Benign	0.46
PhyloP100		-0.63
PromoterAI		0.0072	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7176005; hg19: chr15-51631279;