rs282802

Variant names:

• chr15-79780478-G-A
• rs282802

Your query was ambiguous. Multiple possible variants found:

• chr15-79780478-G-A
• chr15-79780478-G-C
• chr15-79780478-G-T

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 0.715 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.715 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

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.726

Alfa AF: 0.723 Hom.: 81733

Bravo AF: 0.708

Asia WGS AF: 0.794 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs282802; hg19: chr15-80072820;