rs6507022

chr18-33418167-G-C

Variant summary

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

The NM_001105528.4(CCDC178):c.-22-6057C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,038 control chromosomes in the GnomAD database, including 28,133 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 0.60 (28133 hom., cov: 32)
• Consequence: CCDC178 NM_001105528.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC178	NM_001105528.4	c.-22-6057C>G		intron_variant		ENST00000383096.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC178	ENST00000383096.8	c.-22-6057C>G		intron_variant		5	NM_001105528.4	A2

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90620 AN: 151920 Hom.: 28117 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.596 AC: 90659 AN: 152038 Hom.: 28133 Cov.: 32 AF XY: 0.604 AC XY: 44905 AN XY: 74310

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.617

Alfa AF: 0.617 Hom.: 3670

Bravo AF: 0.587

Asia WGS AF: 0.785 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.0
Dann	Benign	0.74

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: rs6507022; hg19: chr18-30998131;