10-12899157-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031455.4(CCDC3):c.550-478A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,866 control chromosomes in the GnomAD database, including 5,623 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association not found (★).

• Frequency: Genomes: 𝑓 0.26 (5623 hom., cov: 31)
• Consequence: CCDC3 NM_031455.4 intron
• Clinical Significance: association not found criteria provided, single submitter O:1
• Conservation: PhyloP100: -0.707

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC3	NM_031455.4	c.550-478A>G		intron_variant		ENST00000378825.5
CCDC3	NM_001282658.2	c.175-478A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC3	ENST00000378825.5	c.550-478A>G		intron_variant		1	NM_031455.4	P1
	ENST00000649832.1	n.710+446T>C		intron_variant, non_coding_transcript_variant
CCDC3	ENST00000378839.1	c.175-478A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40129 AN: 151750 Hom.: 5619 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.264 AC: 40164 AN: 151866 Hom.: 5623 Cov.: 31 AF XY: 0.270 AC XY: 20044 AN XY: 74194

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.238

Alfa AF: 0.223 Hom.: 5176

Bravo AF: 0.261

Asia WGS AF: 0.417 AC: 1449 AN: 3478

ClinVar

Significance: association not found

Submissions summary: Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

Lip and oral cavity carcinoma Other:1

association not found, criteria provided, single submitter

case-control

Department of Biological Science, Sunandan Divatia School of Science, NMIMS University

Nov 02, 2015

No significant association was observed with SNP rs4748011 in CCDC3 and oral cancer. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.47
Dann	Benign	0.41

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

Other links and lift over

dbSNP: rs4748011; hg19: chr10-12941157;