10-13005506-G-A

Position:

• chr10-13005506-G-A

Variant summary

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

The NM_001282658.2(CCDC3):​c.-1-6994C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,124 control chromosomes in the GnomAD database, including 50,869 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 0.81 (50869 hom., cov: 31)
• Consequence: CCDC3 NM_001282658.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC3	NM_001282658.2	c.-1-6994C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC3	ENST00000378839.1	c.-1-6994C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122989 AN: 152006 Hom.: 50825 Cov.: 31

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.809 AC: 123085 AN: 152124 Hom.: 50869 Cov.: 31 AF XY: 0.808 AC XY: 60107 AN XY: 74402

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.904

Gnomad4 NFE AF: 0.887

Gnomad4 OTH AF: 0.831

Alfa AF: 0.861 Hom.: 25827

Bravo AF: 0.801

Asia WGS AF: 0.798 AC: 2777 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	0.29
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs552437; hg19: chr10-13047506;