15-74328398-C-T

Variant names:

• chr15-74328398-C-T
• rs2930306
• NM_025055.5:c.1291-1791C>T

Variant summary

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

The NM_025055.5(CCDC33):​c.1291-1791C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,128 control chromosomes in the GnomAD database, including 32,436 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 0.65 (32436 hom., cov: 33)
• Consequence: CCDC33 NM_025055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC33	NM_025055.5	c.1291-1791C>T		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.1291-1791C>T		intron_variant	Intron 11 of 18	2	NM_025055.5	ENSP00000381795.3

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98556 AN: 152010 Hom.: 32428 Cov.: 33

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.648 AC: 98596 AN: 152128 Hom.: 32436 Cov.: 33 AF XY: 0.643 AC XY: 47837 AN XY: 74368

African (AFR) AF: 0.619 AC: 25681 AN: 41470

American (AMR) AF: 0.482 AC: 7370 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2323 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2498 AN: 5168

South Asian (SAS) AF: 0.551 AC: 2654 AN: 4818

European-Finnish (FIN) AF: 0.750 AC: 7955 AN: 10600

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48149 AN: 67996

Other (OTH) AF: 0.609 AC: 1285 AN: 2110

Alfa AF: 0.678 Hom.: 55236

Bravo AF: 0.628

Asia WGS AF: 0.461 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.41
PhyloP100		-2.2
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: rs2930306; hg19: chr15-74620739;