chr15-62080393-A-G

Variant names:

• chr15-62080393-A-G
• rs12913951

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 0.432 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
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.346 AC: 14347 AN: 41444

American (AMR) AF: 0.528 AC: 8063 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1382 AN: 3470

East Asian (EAS) AF: 0.379 AC: 1959 AN: 5172

South Asian (SAS) AF: 0.376 AC: 1816 AN: 4826

European-Finnish (FIN) AF: 0.662 AC: 6956 AN: 10512

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29902 AN: 67936

Other (OTH) AF: 0.432 AC: 911 AN: 2110

Alfa AF: 0.383 Hom.: 1800

Bravo AF: 0.421

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.1
DANN	Benign	0.78
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs12913951; hg19: chr15-62372592;