chr15-74281566-G-C

Variant names:

• chr15-74281566-G-C
• rs901130
• NM_025055.5:c.1024-212G>C

Variant summary

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

The NM_025055.5(CCDC33):​c.1024-212G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,202 control chromosomes in the GnomAD database, including 24,926 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 0.51 (24926 hom., cov: 33)
• Consequence: CCDC33 NM_025055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 6 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025055.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC33	NM_025055.5	MANE Select	c.1024-212G>C		intron	N/A	NP_079331.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC33	ENST00000398814.8	TSL:2 MANE Select	c.1024-212G>C		intron	N/A	ENSP00000381795.3
	CCDC33	ENST00000558659.5	TSL:1	c.664-212G>C		intron	N/A	ENSP00000453542.1
	CCDC33	ENST00000635913.2	TSL:5	c.1678-212G>C		intron	N/A	ENSP00000490425.2

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78392 AN: 152086 Hom.: 24936 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.515 AC: 78374 AN: 152202 Hom.: 24926 Cov.: 33 AF XY: 0.514 AC XY: 38285 AN XY: 74412

African (AFR) AF: 0.145 AC: 6023 AN: 41530

American (AMR) AF: 0.468 AC: 7151 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1997 AN: 3470

East Asian (EAS) AF: 0.498 AC: 2582 AN: 5182

South Asian (SAS) AF: 0.435 AC: 2096 AN: 4818

European-Finnish (FIN) AF: 0.794 AC: 8419 AN: 10598

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48420 AN: 67992

Other (OTH) AF: 0.505 AC: 1069 AN: 2116

Alfa AF: 0.514 Hom.: 2032

Bravo AF: 0.476

Asia WGS AF: 0.398 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs901130; hg19: chr15-74573907;