15-92377797-C-T

Variant names:

• chr15-92377797-C-T
• rs4586379

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 0.77 in 152,044 control chromosomes in the GnomAD database, including 45,206 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 0.77 (45206 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.775 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: 0.770 AC: 116937 AN: 151926 Hom.: 45142 Cov.: 30

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.770 AC: 117063 AN: 152044 Hom.: 45206 Cov.: 30 AF XY: 0.773 AC XY: 57507 AN XY: 74348

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.777

Alfa AF: 0.766 Hom.: 13035

Bravo AF: 0.766

Asia WGS AF: 0.772 AC: 2686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4586379; hg19: chr15-92921027;