15-92507736-A-G

Variant names:

• chr15-92507736-A-G
• rs1455782

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 0.788 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.788 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

African (AFR) AF: 0.900 AC: 37356 AN: 41516

American (AMR) AF: 0.807 AC: 12342 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2451 AN: 3470

East Asian (EAS) AF: 0.901 AC: 4673 AN: 5186

South Asian (SAS) AF: 0.761 AC: 3665 AN: 4818

European-Finnish (FIN) AF: 0.773 AC: 8169 AN: 10568

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48804 AN: 67954

Other (OTH) AF: 0.775 AC: 1640 AN: 2116

Alfa AF: 0.743 Hom.: 108370

Bravo AF: 0.796

Asia WGS AF: 0.846 AC: 2942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.4
DANN	Benign	0.79
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1455782; hg19: chr15-93050966;