rs2930313

chr15-74317037-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CCDC33	NM_025055.5	c.1291-13152A>G		intron_variant		ENST00000398814.8
LOC124903525	XR_007064711.1	n.173+2483T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC33	ENST00000398814.8	c.1291-13152A>G		intron_variant		2	NM_025055.5	P2
CCDC33	ENST00000558659.5	c.932-13152A>G		intron_variant		1
	ENST00000611006.1	n.169+2483T>C		intron_variant, non_coding_transcript_variant		2
CCDC33	ENST00000635913.2	c.1945-13152A>G		intron_variant		5		A2

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

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0844

Gnomad4 NFE AF: 0.0790

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0892 Hom.: 649

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2930313; hg19: chr15-74609378;