chr15-74256432-G-A

Variant names:

• chr15-74256432-G-A
• rs9783698
• NM_025055.5:c.186-6008G>A

Variant summary

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

The NM_025055.5(CCDC33):​c.186-6008G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,836 control chromosomes in the GnomAD database, including 8,892 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 0.33 (8892 hom., cov: 33)
• Consequence: CCDC33 NM_025055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 12 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC33	NM_025055.5	c.186-6008G>A		intron_variant	Intron 2 of 18	ENST00000398814.8	NP_079331.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC33	ENST00000398814.8	c.186-6008G>A		intron_variant	Intron 2 of 18	2	NM_025055.5	ENSP00000381795.3
CCDC33	ENST00000635913.2	c.840-6008G>A		intron_variant	Intron 3 of 19	5		ENSP00000490425.2

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50287 AN: 151716 Hom.: 8880 Cov.: 33

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.331 AC: 50318 AN: 151836 Hom.: 8892 Cov.: 33 AF XY: 0.334 AC XY: 24801 AN XY: 74196

African (AFR) AF: 0.448 AC: 18530 AN: 41376

American (AMR) AF: 0.198 AC: 3031 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3466

East Asian (EAS) AF: 0.453 AC: 2334 AN: 5150

South Asian (SAS) AF: 0.443 AC: 2131 AN: 4808

European-Finnish (FIN) AF: 0.331 AC: 3488 AN: 10544

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18596 AN: 67910

Other (OTH) AF: 0.292 AC: 617 AN: 2110

Alfa AF: 0.293 Hom.: 22054

Bravo AF: 0.324

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.61
DANN	Benign	0.70
PhyloP100		-0.43
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: rs9783698; hg19: chr15-74548773;