rs479062

Positions:

• chr15-49798059-A-C
• chr15-49798059-A-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 0.544 in 152,030 control chromosomes in the GnomAD database, including 22,596 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 0.54 (22596 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 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: 0.544 AC: 82679 AN: 151912 Hom.: 22590 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.544 AC: 82714 AN: 152030 Hom.: 22596 Cov.: 32 AF XY: 0.539 AC XY: 40027 AN XY: 74306

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.536

Alfa AF: 0.543 Hom.: 29950

Bravo AF: 0.542

Asia WGS AF: 0.404 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs479062; hg19: chr15-50090256;