rs6507022

Variant names:

• chr18-33418167-G-C
• rs6507022
• NM_001105528.4:c.-22-6057C>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.-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
• 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC178	NM_001105528.4	c.-22-6057C>G		intron_variant	Intron 2 of 22	ENST00000383096.8	NP_001098998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC178	ENST00000383096.8	c.-22-6057C>G		intron_variant	Intron 2 of 22	5	NM_001105528.4	ENSP00000372576.3

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

African (AFR) AF: 0.417 AC: 17290 AN: 41460

American (AMR) AF: 0.710 AC: 10841 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2101 AN: 3470

East Asian (EAS) AF: 0.800 AC: 4136 AN: 5168

South Asian (SAS) AF: 0.773 AC: 3733 AN: 4832

European-Finnish (FIN) AF: 0.718 AC: 7576 AN: 10554

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42859 AN: 67960

Other (OTH) AF: 0.617 AC: 1306 AN: 2116

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
PhyloP100		0.25
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: rs6507022; hg19: chr18-30998131;