rs7176093

Variant names:

• chr15-85826199-G-A
• rs7176093

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 0.233 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
• Publications: 10 publications found

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 = 0.272 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.193 AC: 8009 AN: 41528

American (AMR) AF: 0.214 AC: 3264 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3470

East Asian (EAS) AF: 0.0942 AC: 488 AN: 5180

South Asian (SAS) AF: 0.140 AC: 677 AN: 4824

European-Finnish (FIN) AF: 0.258 AC: 2734 AN: 10586

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18705 AN: 68002

Other (OTH) AF: 0.231 AC: 488 AN: 2114

Alfa AF: 0.253 Hom.: 9904

Bravo AF: 0.228

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.75
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs7176093; hg19: chr15-86369430;