18-33263452-C-T

Position:

• chr18-33263452-C-T

Variant summary

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

The NM_001105528.4(CCDC178):​c.1409+3464G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,002 control chromosomes in the GnomAD database, including 1,317 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 0.11 (1317 hom., cov: 32)
• Consequence: CCDC178 NM_001105528.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

CCDC178 (HGNC:29588): (coiled-coil domain containing 178) Located in ciliary basal body. [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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC178	NM_001105528.4	c.1409+3464G>A		intron_variant		ENST00000383096.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC178	ENST00000383096.8	c.1409+3464G>A		intron_variant		5	NM_001105528.4	A2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16654 AN: 151884 Hom.: 1317 Cov.: 32

Gnomad AFR AF: 0.0283

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0582

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.110 AC: 16656 AN: 152002 Hom.: 1317 Cov.: 32 AF XY: 0.111 AC XY: 8225 AN XY: 74256

Gnomad4 AFR AF: 0.0282

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.0582

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.126

Alfa AF: 0.136 Hom.: 1399

Bravo AF: 0.111

Asia WGS AF: 0.227 AC: 784 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.79
DANN	Benign	0.47

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: rs12606061; hg19: chr18-30843416;