rs7176093

chr15-85826199-G-A

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 0.233 in 152,192 control chromosomes in the GnomAD database, including 4,281 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 (4281 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812

ACMG classification

Verdict is Benign. Variant got -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 = 0.272 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: 0.234 AC: 35517 AN: 152074 Hom.: 4283 Cov.: 34

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.233 AC: 35524 AN: 152192 Hom.: 4281 Cov.: 34 AF XY: 0.227 AC XY: 16899 AN XY: 74398

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0942

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.231

Alfa AF: 0.259 Hom.: 6784

Bravo AF: 0.228

Asia WGS AF: 0.0970 AC: 338 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	5.2
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7176093; hg19: chr15-86369430;