15-74328398-C-T

Position:

• chr15-74328398-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

CCDC33 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CCDC33	NM_025055.5	c.1291-1791C>T		intron_variant		ENST00000398814.8	NP_079331.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC33	ENST00000398814.8	c.1291-1791C>T		intron_variant		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

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.609

Alfa AF: 0.684 Hom.: 47030

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

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: rs2930306; hg19: chr15-74620739;