15-74324375-T-C

Variant names:

• chr15-74324375-T-C
• rs2930300
• NM_025055.5:c.1291-5814T>C

Variant summary

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

The NM_025055.5(CCDC33):​c.1291-5814T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,578 control chromosomes in the GnomAD database, including 25,011 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 0.56 (25011 hom., cov: 28)
• Consequence: CCDC33 NM_025055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC33	NM_025055.5	c.1291-5814T>C		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.1291-5814T>C		intron_variant	Intron 11 of 18	2	NM_025055.5	ENSP00000381795.3

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84817 AN: 151458 Hom.: 25009 Cov.: 28

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.560 AC: 84853 AN: 151578 Hom.: 25011 Cov.: 28 AF XY: 0.554 AC XY: 41068 AN XY: 74066

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.546

Alfa AF: 0.614 Hom.: 3545

Bravo AF: 0.550

Asia WGS AF: 0.330 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.82
DANN	Benign	0.33

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: rs2930300; hg19: chr15-74616716;