15-99564180-C-T

Variant names:

• chr15-99564180-C-T
• rs4424892

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 0.765 in 152,058 control chromosomes in the GnomAD database, including 44,990 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 0.76 (44990 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.839 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: 0.765 AC: 116204 AN: 151940 Hom.: 44955 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.765 AC: 116293 AN: 152058 Hom.: 44990 Cov.: 31 AF XY: 0.769 AC XY: 57177 AN XY: 74340

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.786

Alfa AF: 0.774 Hom.: 7518

Bravo AF: 0.749

Asia WGS AF: 0.794 AC: 2758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4424892; hg19: chr15-100104385;