rs2930291

Variant names:

• chr15-74312493-G-A
• rs2930291
• NM_025055.5:c.1290+16545G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-74312493-G-A
• chr15-74312493-G-C

Variant summary

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

The NM_025055.5(CCDC33):​c.1290+16545G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,996 control chromosomes in the GnomAD database, including 18,175 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 0.47 (18175 hom., cov: 31)
• Consequence: CCDC33 NM_025055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77
• Publications: 11 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]

ENSG00000277749 (HGNC:58163):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC33	NM_025055.5	c.1290+16545G>A		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.1290+16545G>A		intron_variant	Intron 11 of 18	2	NM_025055.5	ENSP00000381795.3
CCDC33	ENST00000558659.5	c.930+16545G>A		intron_variant	Intron 8 of 16	1		ENSP00000453542.1
CCDC33	ENST00000635913.2	c.1944+16545G>A		intron_variant	Intron 12 of 19	5		ENSP00000490425.2
ENSG00000277749	ENST00000611006.2	n.198-535C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71253 AN: 151878 Hom.: 18146 Cov.: 31

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.469 AC: 71341 AN: 151996 Hom.: 18175 Cov.: 31 AF XY: 0.474 AC XY: 35188 AN XY: 74298

African (AFR) AF: 0.635 AC: 26317 AN: 41432

American (AMR) AF: 0.431 AC: 6581 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1513 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3818 AN: 5156

South Asian (SAS) AF: 0.688 AC: 3309 AN: 4810

European-Finnish (FIN) AF: 0.294 AC: 3108 AN: 10582

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25078 AN: 67960

Other (OTH) AF: 0.483 AC: 1018 AN: 2106

Alfa AF: 0.408 Hom.: 5612

Bravo AF: 0.482

Asia WGS AF: 0.723 AC: 2516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		1.8
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: rs2930291; hg19: chr15-74604834;