15-79780478-G-A

Variant names:

• chr15-79780478-G-A
• rs282802

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 0.715 in 152,160 control chromosomes in the GnomAD database, including 39,110 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 0.72 (39110 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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: 0.715 AC: 108721 AN: 152042 Hom.: 39069 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.715 AC: 108816 AN: 152160 Hom.: 39110 Cov.: 33 AF XY: 0.717 AC XY: 53327 AN XY: 74380

African (AFR) AF: 0.686 AC: 28488 AN: 41500

American (AMR) AF: 0.689 AC: 10538 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2456 AN: 3470

East Asian (EAS) AF: 0.836 AC: 4319 AN: 5168

South Asian (SAS) AF: 0.779 AC: 3758 AN: 4822

European-Finnish (FIN) AF: 0.722 AC: 7639 AN: 10584

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49366 AN: 68000

Other (OTH) AF: 0.726 AC: 1534 AN: 2114

Alfa AF: 0.721 Hom.: 120934

Bravo AF: 0.708

Asia WGS AF: 0.794 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.82
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs282802; hg19: chr15-80072820;