rs8033165

Positions:

• chr15-28760947-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.313 in 150,274 control chromosomes in the GnomAD database, including 8,695 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 0.31 (8695 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.23

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 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: 0.313 AC: 46962 AN: 150158 Hom.: 8694 Cov.: 28

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.00118

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.313 AC: 46966 AN: 150274 Hom.: 8695 Cov.: 28 AF XY: 0.306 AC XY: 22464 AN XY: 73330

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.00118

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.269

Alfa AF: 0.393 Hom.: 5282

Bravo AF: 0.287

Asia WGS AF: 0.100 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	23
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8033165; hg19: chr15-29006093;