chr15-74336550-A-G

Variant names:

• chr15-74336550-A-G
• rs2959003
• ENST00000558659.5:c.*93A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558659.5(CCDC33):​c.*93A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 728,814 control chromosomes in the GnomAD database, including 146,989 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 0.56 (24984 hom., cov: 33)
  • Exomes 𝑓: 0.64 (122005 hom.)
• Consequence: CCDC33 ENST00000558659.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596
• Publications: 12 publications found

Genes affected

CCDC33 (HGNC:26552): (coiled-coil domain containing 33) Predicted to be active in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558659.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC33	ENST00000558659.5	TSL:1	c.*93A>G		downstream_gene	N/A	ENSP00000453542.1	H0YMB8

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85104 AN: 151964 Hom.: 24973 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.531

GnomAD4 exome AF: 0.643 AC: 370914 AN: 576732 Hom.: 122005 AF XY: 0.635 AC XY: 184248 AN XY: 290064

African (AFR) AF: 0.435 AC: 5173 AN: 11890

American (AMR) AF: 0.353 AC: 4405 AN: 12468

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 4198 AN: 7118

East Asian (EAS) AF: 0.350 AC: 3192 AN: 9112

South Asian (SAS) AF: 0.473 AC: 23933 AN: 50608

European-Finnish (FIN) AF: 0.691 AC: 6724 AN: 9724

Middle Eastern (MID) AF: 0.490 AC: 1533 AN: 3128

European-Non Finnish (NFE) AF: 0.684 AC: 308318 AN: 450660

Other (OTH) AF: 0.610 AC: 13438 AN: 22024

GnomAD4 genome AF: 0.560 AC: 85149 AN: 152082 Hom.: 24984 Cov.: 33 AF XY: 0.552 AC XY: 40994 AN XY: 74322

African (AFR) AF: 0.436 AC: 18099 AN: 41470

American (AMR) AF: 0.415 AC: 6347 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2069 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1850 AN: 5166

South Asian (SAS) AF: 0.454 AC: 2190 AN: 4820

European-Finnish (FIN) AF: 0.682 AC: 7204 AN: 10568

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.673 AC: 45781 AN: 67982

Other (OTH) AF: 0.526 AC: 1112 AN: 2114

Alfa AF: 0.613 Hom.: 39054

Bravo AF: 0.535

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.64
PhyloP100		0.60
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2959003; hg19: chr15-74628891; COSMIC: COSV51431951;