rs7176005

Positions:

• chr15-51339082-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.0637

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.202

Alfa AF: 0.147 Hom.: 554

Bravo AF: 0.227

Asia WGS AF: 0.290 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.2
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7176005; hg19: chr15-51631279;