18-33347811-C-T

Variant names:

• chr18-33347811-C-T
• rs6507016
• NM_001105528.4:c.457+1079G>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.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
• Publications: 11 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001105528.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC178	NM_001105528.4	MANE Select	c.457+1079G>A		intron	N/A	NP_001098998.1
	CCDC178	NM_001308126.3		c.457+1079G>A		intron	N/A	NP_001295055.1
	CCDC178	NM_001371120.1		c.457+1079G>A		intron	N/A	NP_001358049.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC178	ENST00000383096.8	TSL:5 MANE Select	c.457+1079G>A		intron	N/A	ENSP00000372576.3
	CCDC178	ENST00000583930.5	TSL:1	c.457+1079G>A		intron	N/A	ENSP00000463254.1
	CCDC178	ENST00000403303.5	TSL:1	c.457+1079G>A		intron	N/A	ENSP00000385591.1

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

African (AFR) AF: 0.647 AC: 26796 AN: 41434

American (AMR) AF: 0.451 AC: 6882 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3464

East Asian (EAS) AF: 0.481 AC: 2480 AN: 5160

South Asian (SAS) AF: 0.387 AC: 1863 AN: 4816

European-Finnish (FIN) AF: 0.308 AC: 3240 AN: 10516

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21386 AN: 67750

Other (OTH) AF: 0.419 AC: 881 AN: 2104

Alfa AF: 0.360 Hom.: 23947

Bravo AF: 0.454

Asia WGS AF: 0.474 AC: 1642 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.3
DANN	Benign	0.28
PhyloP100		0.025
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: rs6507016; hg19: chr18-30927775; COSMIC: COSV55757113;