rs2930313

Variant names:

• chr15-74317037-A-G
• rs2930313
• NM_025055.5:c.1291-13152A>G

Variant summary

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

The NM_025055.5(CCDC33):​c.1291-13152A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,120 control chromosomes in the GnomAD database, including 1,087 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 0.11 (1087 hom., cov: 32)
• Consequence: CCDC33 NM_025055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 5 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]

ENSG00000277749 (HGNC:58163):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC33	NM_025055.5	c.1291-13152A>G		intron_variant	Intron 11 of 18	ENST00000398814.8	NP_079331.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC33	ENST00000398814.8	c.1291-13152A>G		intron_variant	Intron 11 of 18	2	NM_025055.5	ENSP00000381795.3
CCDC33	ENST00000558659.5	c.931-13152A>G		intron_variant	Intron 8 of 16	1		ENSP00000453542.1
CCDC33	ENST00000635913.2	c.1945-13152A>G		intron_variant	Intron 12 of 19	5		ENSP00000490425.2
ENSG00000277749	ENST00000611006.2	n.197+2483T>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17034 AN: 152000 Hom.: 1082 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0789

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.112 AC: 17047 AN: 152120 Hom.: 1087 Cov.: 32 AF XY: 0.114 AC XY: 8457 AN XY: 74372

African (AFR) AF: 0.143 AC: 5928 AN: 41486

American (AMR) AF: 0.131 AC: 1999 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3472

East Asian (EAS) AF: 0.282 AC: 1459 AN: 5170

South Asian (SAS) AF: 0.133 AC: 641 AN: 4822

European-Finnish (FIN) AF: 0.0844 AC: 893 AN: 10582

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0790 AC: 5369 AN: 67986

Other (OTH) AF: 0.109 AC: 229 AN: 2110

Alfa AF: 0.0947 Hom.: 1124

Bravo AF: 0.119

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.65
PhyloP100		-0.47
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: rs2930313; hg19: chr15-74609378;