chr18-32984676-T-C

Position:

• chr18-32984676-T-C

Variant summary

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

The NM_001105528.4(CCDC178):​c.2389-9995A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.096 in 151,854 control chromosomes in the GnomAD database, including 1,037 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 0.096 (1037 hom., cov: 32)
• Consequence: CCDC178 NM_001105528.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC178	NM_001105528.4	c.2389-9995A>G		intron_variant		ENST00000383096.8	NP_001098998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC178	ENST00000383096.8	c.2389-9995A>G		intron_variant		5	NM_001105528.4	ENSP00000372576.3

Frequencies

GnomAD3 genomes AF: 0.0959 AC: 14551 AN: 151736 Hom.: 1030 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0798

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0302

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0618

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0960 AC: 14583 AN: 151854 Hom.: 1037 Cov.: 32 AF XY: 0.0936 AC XY: 6950 AN XY: 74234

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.0797

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0201

Gnomad4 FIN AF: 0.0302

Gnomad4 NFE AF: 0.0618

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0364 Hom.: 19

Bravo AF: 0.103

Asia WGS AF: 0.0220 AC: 75 AN: 3408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.87
DANN	Benign	0.40

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: rs9958315; hg19: chr18-30564640;