15-48372356-C-T

Variant names:

• chr15-48372356-C-T
• rs5020564

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 0.182 in 152,024 control chromosomes in the GnomAD database, including 2,717 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 0.18 (2717 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 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: 0.182 AC: 27639 AN: 151906 Hom.: 2714 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.182 AC: 27668 AN: 152024 Hom.: 2717 Cov.: 31 AF XY: 0.183 AC XY: 13581 AN XY: 74314

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.204

Alfa AF: 0.168 Hom.: 508

Bravo AF: 0.185

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.73
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5020564; hg19: chr15-48664553;