18-33263452-C-T

Variant names:

• chr18-33263452-C-T
• rs12606061
• NM_001105528.4:c.1409+3464G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC178	NM_001105528.4	c.1409+3464G>A		intron_variant	Intron 14 of 22	ENST00000383096.8	NP_001098998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC178	ENST00000383096.8	c.1409+3464G>A		intron_variant	Intron 14 of 22	5	NM_001105528.4	ENSP00000372576.3

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

African (AFR) AF: 0.0282 AC: 1170 AN: 41500

American (AMR) AF: 0.133 AC: 2025 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3472

East Asian (EAS) AF: 0.335 AC: 1725 AN: 5150

South Asian (SAS) AF: 0.217 AC: 1042 AN: 4806

European-Finnish (FIN) AF: 0.0582 AC: 614 AN: 10548

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9318 AN: 67956

Other (OTH) AF: 0.126 AC: 266 AN: 2112

Alfa AF: 0.135 Hom.: 1634

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
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12606061; hg19: chr18-30843416;