18-33347811-C-T

Position:

• chr18-33347811-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.457+1079G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,698 control chromosomes in the GnomAD database, including 15,565 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 0.43 (15565 hom., cov: 32)
• Consequence: CCDC178 NM_001105528.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC178	NM_001105528.4	c.457+1079G>A		intron_variant		ENST00000383096.8	NP_001098998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC178	ENST00000383096.8	c.457+1079G>A		intron_variant		5	NM_001105528.4	ENSP00000372576	A2

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65161 AN: 151580 Hom.: 15503 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.430 AC: 65293 AN: 151698 Hom.: 15565 Cov.: 32 AF XY: 0.429 AC XY: 31796 AN XY: 74110

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.419

Alfa AF: 0.348 Hom.: 4367

Bravo AF: 0.454

Asia WGS AF: 0.474 AC: 1642 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.3
DANN	Benign	0.28

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: rs6507016; hg19: chr18-30927775; COSMIC: COSV55757113; COSMIC: COSV55757113;