rs4436849

chr18-32975482-C-Achr18-32975482-C-Gchr18-32975482-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.2389-801G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,108 control chromosomes in the GnomAD database, including 54,052 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 0.80 (54052 hom., cov: 32)
• Consequence: CCDC178 NM_001105528.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC178	NM_001105528.4	c.2389-801G>T		intron_variant		ENST00000383096.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC178	ENST00000383096.8	c.2389-801G>T		intron_variant		5	NM_001105528.4	A2

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121557 AN: 151990 Hom.: 54056 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.799 AC: 121572 AN: 152108 Hom.: 54052 Cov.: 32 AF XY: 0.803 AC XY: 59723 AN XY: 74384

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.979

Gnomad4 OTH AF: 0.857

Alfa AF: 0.939 Hom.: 67258

Bravo AF: 0.777

Asia WGS AF: 0.883 AC: 3069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.2
Dann	Benign	0.49

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: rs4436849; hg19: chr18-30555446;