15-90822992-G-A

Variant names:

• chr15-90822992-G-A
• rs441399

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 0.501 in 151,964 control chromosomes in the GnomAD database, including 19,849 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 0.50 (19849 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 14 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 (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76097 AN: 151846 Hom.: 19843 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.501 AC: 76142 AN: 151964 Hom.: 19849 Cov.: 31 AF XY: 0.504 AC XY: 37446 AN XY: 74276

African (AFR) AF: 0.364 AC: 15084 AN: 41428

American (AMR) AF: 0.582 AC: 8880 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1948 AN: 3472

East Asian (EAS) AF: 0.726 AC: 3746 AN: 5160

South Asian (SAS) AF: 0.535 AC: 2581 AN: 4826

European-Finnish (FIN) AF: 0.521 AC: 5498 AN: 10554

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36639 AN: 67964

Other (OTH) AF: 0.497 AC: 1045 AN: 2104

Alfa AF: 0.528 Hom.: 36928

Bravo AF: 0.501

Asia WGS AF: 0.598 AC: 2077 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	0.22
DANN	Benign	0.32
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs441399; hg19: chr15-91366222;