rs17739703

Variant names:

• chr18-32943324-T-C
• rs17739703
• NM_001105528.4:c.2524-5233A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001105528.4(CCDC178):​c.2524-5233A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0464 in 152,172 control chromosomes in the GnomAD database, including 218 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 0.046 (218 hom., cov: 32)
• Consequence: CCDC178 NM_001105528.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 4 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]

LOC105372059 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0712 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.2524-5233A>G		intron	N/A	NP_001098998.1
	CCDC178	NM_001308126.3		c.2596-5233A>G		intron	N/A	NP_001295055.1
	CCDC178	NM_001371120.1		c.2596-5233A>G		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.2524-5233A>G		intron	N/A	ENSP00000372576.3
	CCDC178	ENST00000583930.5	TSL:1	c.2596-5233A>G		intron	N/A	ENSP00000463254.1
	CCDC178	ENST00000403303.5	TSL:1	c.2524-5233A>G		intron	N/A	ENSP00000385591.1

Frequencies

GnomAD3 genomes AF: 0.0465 AC: 7067 AN: 152054 Hom.: 218 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0729

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0464 AC: 7064 AN: 152172 Hom.: 218 Cov.: 32 AF XY: 0.0453 AC XY: 3370 AN XY: 74408

African (AFR) AF: 0.0126 AC: 523 AN: 41538

American (AMR) AF: 0.0251 AC: 384 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0189 AC: 91 AN: 4822

European-Finnish (FIN) AF: 0.0839 AC: 888 AN: 10586

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0729 AC: 4958 AN: 67992

Other (OTH) AF: 0.0265 AC: 56 AN: 2110

Alfa AF: 0.0649 Hom.: 197

Bravo AF: 0.0408

Asia WGS AF: 0.00953 AC: 33 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.25
PhyloP100		-0.073
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: rs17739703; hg19: chr18-30523288;