rs479062

Variant names:

• chr15-49798059-A-C
• rs479062

Your query was ambiguous. Multiple possible variants found:

• chr15-49798059-A-C
• chr15-49798059-A-G
• chr15-49798059-A-T

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 0.544 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.576 AC: 23898 AN: 41466

American (AMR) AF: 0.487 AC: 7440 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1661 AN: 3470

East Asian (EAS) AF: 0.475 AC: 2456 AN: 5166

South Asian (SAS) AF: 0.444 AC: 2143 AN: 4828

European-Finnish (FIN) AF: 0.534 AC: 5635 AN: 10550

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37535 AN: 67956

Other (OTH) AF: 0.536 AC: 1131 AN: 2110

Alfa AF: 0.544 Hom.: 47496

Bravo AF: 0.542

Asia WGS AF: 0.404 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.9
DANN	Benign	0.72
PhyloP100		0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs479062;

hg19: chr15-50090256;