rs8029801

chr15-101533714-C-T

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 0.189 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.155

Alfa AF: 0.171 Hom.: 2374

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8029801; hg19: chr15-102073917;