rs8033556

Variant names:

• chr15-48350109-A-G
• rs8033556

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 0.789 in 151,988 control chromosomes in the GnomAD database, including 47,737 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 0.79 (47737 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.833 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: 0.789 AC: 119886 AN: 151870 Hom.: 47726 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.789 AC: 119942 AN: 151988 Hom.: 47737 Cov.: 31 AF XY: 0.789 AC XY: 58590 AN XY: 74300

African (AFR) AF: 0.736 AC: 30484 AN: 41434

American (AMR) AF: 0.739 AC: 11274 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2802 AN: 3468

East Asian (EAS) AF: 0.563 AC: 2899 AN: 5152

South Asian (SAS) AF: 0.762 AC: 3670 AN: 4814

European-Finnish (FIN) AF: 0.865 AC: 9151 AN: 10582

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 56992 AN: 67964

Other (OTH) AF: 0.764 AC: 1610 AN: 2108

Alfa AF: 0.812 Hom.: 5800

Bravo AF: 0.777

Asia WGS AF: 0.639 AC: 2224 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	0.27
DANN	Benign	0.29
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs8033556; hg19: chr15-48642306;