chr15-85826199-G-A

Variant names:

• chr15-85826199-G-A
• rs7176093

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;