dbSNP rs2959003: CCDC33:c.*93A>G (chr15-74336550-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000558659.5(CCDC33):c.*93A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 728,814 control chromosomes in the GnomAD database, including 146,989 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 ( 24984 hom., cov: 33)

Exomes 𝑓: 0.64 ( 122005 hom. )

Consequence

CCDC33
ENST00000558659.5 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.596

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
CCDC33	XM_011522085.4 link	c.*93A>G	downstream_gene_variant	XP_011520387.1
CCDC33	XM_017022624.2 link	c.*93A>G	downstream_gene_variant	XP_016878113.1
CCDC33	XM_047433141.1 link	c.*93A>G	downstream_gene_variant	XP_047289097.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC33	ENST00000558659.5 link	c.*93A>G		downstream_gene_variant		1		ENSP00000453542.1		H0YMB8

Frequencies

GnomAD3 genomes

AF:

0.560

AC:

85104

AN:

151964

Hom.:

24973

Cov.:

show subpopulations

Gnomad AFR

AF:

0.436

Gnomad AMI

AF:

0.378

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.597

Gnomad EAS

AF:

0.357

Gnomad SAS

AF:

0.455

Gnomad FIN

AF:

0.682

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.673

Gnomad OTH

AF:

0.531

GnomAD4 exome

AF:

0.643

AC:

370914

AN:

576732

Hom.:

122005

AF XY:

0.635

AC XY:

184248

AN XY:

290064

show subpopulations

Gnomad4 AFR exome

AF:

0.435

Gnomad4 AMR exome

AF:

0.353

Gnomad4 ASJ exome

AF:

0.590

Gnomad4 EAS exome

AF:

0.350

Gnomad4 SAS exome

AF:

0.473

Gnomad4 FIN exome

AF:

0.691

Gnomad4 NFE exome

AF:

0.684

Gnomad4 OTH exome

AF:

0.610

GnomAD4 genome

AF:

0.560

AC:

85149

AN:

152082

Hom.:

24984

Cov.:

AF XY:

0.552

AC XY:

40994

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.436

Gnomad4 AMR

AF:

0.415

Gnomad4 ASJ

AF:

0.597

Gnomad4 EAS

AF:

0.358

Gnomad4 SAS

AF:

0.454

Gnomad4 FIN

AF:

0.682

Gnomad4 NFE

AF:

0.673

Gnomad4 OTH

AF:

0.526

Alfa

AF:

0.622

Hom.:

30768

Bravo

AF:

0.535

Asia WGS

AF:

0.386

AC:

1341

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.0

DANN

Benign

0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over