rs282802

chr15-79780478-G-Achr15-79780478-G-Cchr15-79780478-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;