chr15-59862566-A-G

Variant names:

• chr15-59862566-A-G
• rs1437480

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 0.918 in 152,294 control chromosomes in the GnomAD database, including 64,612 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 0.92 (64612 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.918 AC: 139647 AN: 152176 Hom.: 64576 Cov.: 33

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.966

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.918 AC: 139735 AN: 152294 Hom.: 64612 Cov.: 33 AF XY: 0.915 AC XY: 68172 AN XY: 74468

African (AFR) AF: 0.845 AC: 35089 AN: 41544

American (AMR) AF: 0.945 AC: 14460 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.966 AC: 3354 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3178 AN: 5176

South Asian (SAS) AF: 0.900 AC: 4333 AN: 4816

European-Finnish (FIN) AF: 0.947 AC: 10063 AN: 10622

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.973 AC: 66234 AN: 68038

Other (OTH) AF: 0.909 AC: 1921 AN: 2114

Alfa AF: 0.955 Hom.: 87178

Bravo AF: 0.913

Asia WGS AF: 0.750 AC: 2611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.2
DANN	Benign	0.78
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs1437480; hg19: chr15-60154765;