rs441399

chr15-90822992-G-A

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 0.501 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.501 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

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.497

Alfa AF: 0.532 Hom.: 29708

Bravo AF: 0.501

Asia WGS AF: 0.598 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.22
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs441399; hg19: chr15-91366222;