15-80139880-A-G

Position:

• chr15-80139880-A-G

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 0.564 in 152,082 control chromosomes in the GnomAD database, including 25,454 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 0.56 (25454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85682 AN: 151964 Hom.: 25453 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.0906

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.564 AC: 85715 AN: 152082 Hom.: 25454 Cov.: 32 AF XY: 0.558 AC XY: 41524 AN XY: 74360

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.0910

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.570

Alfa AF: 0.624 Hom.: 55863

Bravo AF: 0.554

Asia WGS AF: 0.371 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11634397; hg19: chr15-80432222;