15-48372356-C-T

Variant names:

• chr15-48372356-C-T
• rs5020564

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.195 AC: 8066 AN: 41444

American (AMR) AF: 0.192 AC: 2926 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3470

East Asian (EAS) AF: 0.403 AC: 2082 AN: 5170

South Asian (SAS) AF: 0.236 AC: 1137 AN: 4810

European-Finnish (FIN) AF: 0.138 AC: 1458 AN: 10562

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10845 AN: 67986

Other (OTH) AF: 0.204 AC: 431 AN: 2114

Alfa AF: 0.168 Hom.: 825

Bravo AF: 0.185

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.73
DANN	Benign	0.60
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs5020564; hg19: chr15-48664553;