chr15-33214293-G-A

Variant names:

• chr15-33214293-G-A
• rs7173082

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 0.0801 in 152,086 control chromosomes in the GnomAD database, including 714 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 0.080 (714 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.157 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: 0.0800 AC: 12163 AN: 151968 Hom.: 714 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0706

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0420

Gnomad FIN AF: 0.0206

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.0536

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0801 AC: 12183 AN: 152086 Hom.: 714 Cov.: 32 AF XY: 0.0768 AC XY: 5710 AN XY: 74338

African (AFR) AF: 0.160 AC: 6646 AN: 41440

American (AMR) AF: 0.0706 AC: 1079 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0423 AC: 204 AN: 4826

European-Finnish (FIN) AF: 0.0206 AC: 218 AN: 10562

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0536 AC: 3647 AN: 68000

Other (OTH) AF: 0.0781 AC: 165 AN: 2112

Alfa AF: 0.0695 Hom.: 338

Bravo AF: 0.0887

Asia WGS AF: 0.0240 AC: 83 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.68
DANN	Benign	0.46
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs7173082; hg19: chr15-33506494;