15-80766299-G-A

Variant names:

• chr15-80766299-G-A
• rs12593088

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 0.229 in 152,070 control chromosomes in the GnomAD database, including 4,745 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 (4745 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 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: 0.229 AC: 34798 AN: 151950 Hom.: 4740 Cov.: 31

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.229 AC: 34813 AN: 152070 Hom.: 4745 Cov.: 31 AF XY: 0.228 AC XY: 16964 AN XY: 74340

African (AFR) AF: 0.0843 AC: 3499 AN: 41496

American (AMR) AF: 0.206 AC: 3146 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3472

East Asian (EAS) AF: 0.270 AC: 1393 AN: 5166

South Asian (SAS) AF: 0.317 AC: 1524 AN: 4806

European-Finnish (FIN) AF: 0.274 AC: 2893 AN: 10570

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20408 AN: 67962

Other (OTH) AF: 0.245 AC: 516 AN: 2110

Alfa AF: 0.285 Hom.: 8787

Bravo AF: 0.217

Asia WGS AF: 0.246 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.049
DANN	Benign	0.65
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs12593088; hg19: chr15-81058640;