chr10-13093046-T-C

Variant names:

• chr10-13093046-T-C
• rs10796021
• NM_001282658.2:c.-503+5479A>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.-503+5479A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 135,740 control chromosomes in the GnomAD database, including 13,280 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 0.46 (13280 hom., cov: 24)
• Consequence: CCDC3 NM_001282658.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC3	NM_001282658.2		c.-503+5479A>G		intron	N/A	NP_001269587.1	Q9BQI4-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC3	ENST00000378839.1	TSL:2	c.-503+5479A>G		intron	N/A	ENSP00000368116.1	Q9BQI4-2

Frequencies

GnomAD3 genomes AF: 0.456 AC: 61845 AN: 135712 Hom.: 13290 Cov.: 24

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.575

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.455 AC: 61818 AN: 135740 Hom.: 13280 Cov.: 24 AF XY: 0.447 AC XY: 29283 AN XY: 65544

African (AFR) AF: 0.411 AC: 15378 AN: 37400

American (AMR) AF: 0.491 AC: 6540 AN: 13308

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1693 AN: 3210

East Asian (EAS) AF: 0.289 AC: 1246 AN: 4310

South Asian (SAS) AF: 0.395 AC: 1668 AN: 4222

European-Finnish (FIN) AF: 0.361 AC: 2924 AN: 8100

Middle Eastern (MID) AF: 0.579 AC: 162 AN: 280

European-Non Finnish (NFE) AF: 0.495 AC: 30811 AN: 62222

Other (OTH) AF: 0.517 AC: 961 AN: 1858

Alfa AF: 0.443 Hom.: 8751

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.19
DANN	Benign	0.45
PhyloP100		-0.87
Mutation Taster		=9/91	disease causing (long InDel)

Splicing

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

Other links and lift over

dbSNP: rs10796021; hg19: chr10-13135046;