rs1437480

chr15-59862566-A-G

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 0.918 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.918 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

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.945

Gnomad4 ASJ AF: 0.966

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.947

Gnomad4 NFE AF: 0.973

Gnomad4 OTH AF: 0.909

Alfa AF: 0.959 Hom.: 66966

Bravo AF: 0.913

Asia WGS AF: 0.750 AC: 2611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	5.2
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1437480; hg19: chr15-60154765;