15-101533714-C-T

Variant names:

• chr15-101533714-C-T
• rs8029801

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 0.189 in 152,132 control chromosomes in the GnomAD database, including 2,930 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 0.19 (2930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 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: 0.189 AC: 28718 AN: 152014 Hom.: 2925 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.189 AC: 28758 AN: 152132 Hom.: 2930 Cov.: 32 AF XY: 0.190 AC XY: 14099 AN XY: 74350

African (AFR) AF: 0.253 AC: 10490 AN: 41490

American (AMR) AF: 0.156 AC: 2384 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3470

East Asian (EAS) AF: 0.116 AC: 601 AN: 5178

South Asian (SAS) AF: 0.158 AC: 759 AN: 4808

European-Finnish (FIN) AF: 0.179 AC: 1891 AN: 10584

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11570 AN: 67988

Other (OTH) AF: 0.155 AC: 329 AN: 2116

Alfa AF: 0.173 Hom.: 3554

Bravo AF: 0.189

Asia WGS AF: 0.144 AC: 504 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	0.49
DANN	Benign	0.60
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs8029801; hg19: chr15-102073917;