NM_001282658.2:c.-1-22596C>G

Variant names:

• chr10-13021108-G-C
• rs2580882
• NM_001282658.2:c.-1-22596C>G

Variant summary

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

The NM_001282658.2(CCDC3):​c.-1-22596C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,232 control chromosomes in the GnomAD database, including 1,423 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 0.13 (1423 hom., cov: 33)
• Consequence: CCDC3 NM_001282658.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 1 publications found

Genes affected

CCDC3 (HGNC:23813): (coiled-coil domain containing 3) Involved in negative regulation of gene expression; negative regulation of lipid metabolic process; and negative regulation of tumor necrosis factor-mediated signaling pathway. Located in endoplasmic reticulum and extracellular region. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282658.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC3	NM_001282658.2		c.-1-22596C>G		intron	N/A	NP_001269587.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC3	ENST00000378839.1	TSL:2	c.-1-22596C>G		intron	N/A	ENSP00000368116.1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19861 AN: 152114 Hom.: 1422 Cov.: 33

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.00846

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.130 AC: 19866 AN: 152232 Hom.: 1423 Cov.: 33 AF XY: 0.130 AC XY: 9645 AN XY: 74432

African (AFR) AF: 0.0953 AC: 3960 AN: 41550

American (AMR) AF: 0.127 AC: 1949 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 366 AN: 3468

East Asian (EAS) AF: 0.00829 AC: 43 AN: 5186

South Asian (SAS) AF: 0.143 AC: 687 AN: 4818

European-Finnish (FIN) AF: 0.120 AC: 1272 AN: 10594

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11089 AN: 67996

Other (OTH) AF: 0.132 AC: 279 AN: 2112

Alfa AF: 0.138 Hom.: 178

Bravo AF: 0.128

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.70
PhyloP100		-0.083
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2580882; hg19: chr10-13063108;