15-62080393-A-G

Position:

• chr15-62080393-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 0.432 in 151,948 control chromosomes in the GnomAD database, including 14,783 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 0.43 (14783 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.518 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: 0.432 AC: 65633 AN: 151830 Hom.: 14767 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.432 AC: 65683 AN: 151948 Hom.: 14783 Cov.: 31 AF XY: 0.441 AC XY: 32765 AN XY: 74262

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.432

Alfa AF: 0.385 Hom.: 1759

Bravo AF: 0.421

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12913951; hg19: chr15-62372592;