rs1834018

Positions:

• chr16-58273338-A-G

Variant summary

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

The NM_014157.4(CCDC113):​c.892-5144A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,956 control chromosomes in the GnomAD database, including 1,672 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 0.14 (1672 hom., cov: 32)
• Consequence: CCDC113 NM_014157.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

CCDC113 (HGNC:25002): (cilia and flagella associated protein 263) Involved in cilium assembly. Located in centriolar satellite and ciliary basal body. Part of protein-containing complex. [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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC113	NM_014157.4	c.892-5144A>G		intron_variant		ENST00000219299.8
CCDC113	NM_001142302.2	c.730-5144A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC113	ENST00000219299.8	c.892-5144A>G		intron_variant		1	NM_014157.4	P1
CCDC113	ENST00000443128.6	c.730-5144A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21682 AN: 151838 Hom.: 1662 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.143 AC: 21732 AN: 151956 Hom.: 1672 Cov.: 32 AF XY: 0.148 AC XY: 10976 AN XY: 74280

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.137

Alfa AF: 0.126 Hom.: 2104

Bravo AF: 0.139

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.6
DANN	Benign	0.70

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: rs1834018; hg19: chr16-58307242;