rs6507016

Variant names:

• chr18-33347811-C-A
• rs6507016
• NM_001105528.4:c.457+1079G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-33347811-C-A
• chr18-33347811-C-G
• chr18-33347811-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001105528.4(CCDC178):​c.457+1079G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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>T		intron	N/A	NP_001098998.1
	CCDC178	NM_001308126.3		c.457+1079G>T		intron	N/A	NP_001295055.1
	CCDC178	NM_001371120.1		c.457+1079G>T		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>T		intron	N/A	ENSP00000372576.3
	CCDC178	ENST00000583930.5	TSL:1	c.457+1079G>T		intron	N/A	ENSP00000463254.1
	CCDC178	ENST00000403303.5	TSL:1	c.457+1079G>T		intron	N/A	ENSP00000385591.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.19
PhyloP100		0.025

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;