rs2930291

chr15-74312493-G-Achr15-74312493-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025055.5(CCDC33):c.1290+16545G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,996 control chromosomes in the GnomAD database, including 18,175 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 0.47 (18175 hom., cov: 31)
• Consequence: CCDC33 NM_025055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77

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=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC33	NM_025055.5	c.1290+16545G>A		intron_variant		ENST00000398814.8
LOC124903525	XR_007064711.1	n.174-535C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC33	ENST00000398814.8	c.1290+16545G>A		intron_variant		2	NM_025055.5	P2
CCDC33	ENST00000558659.5	c.931+16545G>A		intron_variant		1
	ENST00000611006.1	n.170-535C>T		intron_variant, non_coding_transcript_variant		2
CCDC33	ENST00000635913.2	c.1944+16545G>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71253 AN: 151878 Hom.: 18146 Cov.: 31

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.469 AC: 71341 AN: 151996 Hom.: 18175 Cov.: 31 AF XY: 0.474 AC XY: 35188 AN XY: 74298

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.483

Alfa AF: 0.405 Hom.: 4559

Bravo AF: 0.482

Asia WGS AF: 0.723 AC: 2516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	12
Dann	Benign	0.70

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: rs2930291; hg19: chr15-74604834;