rs1455782

chr15-92507736-A-Gchr15-92507736-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 0.788 in 152,126 control chromosomes in the GnomAD database, including 47,738 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 0.79 (47738 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 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: 0.788 AC: 119768 AN: 152008 Hom.: 47679 Cov.: 33

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.788 AC: 119891 AN: 152126 Hom.: 47738 Cov.: 33 AF XY: 0.791 AC XY: 58815 AN XY: 74388

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.775

Alfa AF: 0.740 Hom.: 32348

Bravo AF: 0.796

Asia WGS AF: 0.846 AC: 2942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.4
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1455782; hg19: chr15-93050966;