rs441399

Variant names:

• chr15-90822992-G-A
• rs441399

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;