rs8061107

Positions:

• chr16-58267925-C-T

Variant summary

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

The NM_014157.4(CCDC113):​c.891+339C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,556 control chromosomes in the GnomAD database, including 26,985 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 0.59 (26985 hom., cov: 29)
• Consequence: CCDC113 NM_014157.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC113	NM_014157.4	c.891+339C>T		intron_variant		ENST00000219299.8
CCDC113	NM_001142302.2	c.729+339C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC113	ENST00000219299.8	c.891+339C>T		intron_variant		1	NM_014157.4	P1
CCDC113	ENST00000443128.6	c.729+339C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88629 AN: 151436 Hom.: 26966 Cov.: 29

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.585 AC: 88688 AN: 151556 Hom.: 26985 Cov.: 29 AF XY: 0.574 AC XY: 42496 AN XY: 73978

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.549

Alfa AF: 0.591 Hom.: 4489

Bravo AF: 0.590

Asia WGS AF: 0.450 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.96
DANN	Benign	0.43

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: rs8061107; hg19: chr16-58301829;