15-74281566-G-C

Variant summary

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

The NM_025055.5(CCDC33):​c.1024-212G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,202 control chromosomes in the GnomAD database, including 24,926 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 0.51 ( 24926 hom., cov: 33)

Consequence

CCDC33
NM_025055.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.244
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCDC33NM_025055.5 linkc.1024-212G>C intron_variant ENST00000398814.8 NP_079331.3 Q8N5R6-6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCDC33ENST00000398814.8 linkc.1024-212G>C intron_variant 2 NM_025055.5 ENSP00000381795.3 Q8N5R6-6
CCDC33ENST00000558659.5 linkc.664-212G>C intron_variant 1 ENSP00000453542.1 H0YMB8
CCDC33ENST00000635913.2 linkc.1678-212G>C intron_variant 5 ENSP00000490425.2 A0A1B0GV97

Frequencies

GnomAD3 genomes
AF:
0.515
AC:
78392
AN:
152086
Hom.:
24936
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.145
Gnomad AMI
AF:
0.513
Gnomad AMR
AF:
0.468
Gnomad ASJ
AF:
0.576
Gnomad EAS
AF:
0.498
Gnomad SAS
AF:
0.437
Gnomad FIN
AF:
0.794
Gnomad MID
AF:
0.497
Gnomad NFE
AF:
0.712
Gnomad OTH
AF:
0.512
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.515
AC:
78374
AN:
152202
Hom.:
24926
Cov.:
33
AF XY:
0.514
AC XY:
38285
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.145
Gnomad4 AMR
AF:
0.468
Gnomad4 ASJ
AF:
0.576
Gnomad4 EAS
AF:
0.498
Gnomad4 SAS
AF:
0.435
Gnomad4 FIN
AF:
0.794
Gnomad4 NFE
AF:
0.712
Gnomad4 OTH
AF:
0.505
Alfa
AF:
0.514
Hom.:
2032
Bravo
AF:
0.476
Asia WGS
AF:
0.398
AC:
1385
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
1.4
DANN
Benign
0.36

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

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

Other links and lift over

dbSNP: rs901130; hg19: chr15-74573907; API