16-58251299-C-T

Variant names:

• chr16-58251299-C-T
• rs1974876
• NM_014157.4:c.101+1184C>T

Variant summary

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

The NM_014157.4(CFAP263):​c.101+1184C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,266 control chromosomes in the GnomAD database, including 2,090 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 (2090 hom., cov: 33)
• Consequence: CFAP263 NM_014157.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.577

Genes affected

CFAP263 (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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP263	NM_014157.4	c.101+1184C>T		intron_variant	Intron 1 of 8	ENST00000219299.8	NP_054876.2
CFAP263	NM_001142302.2	c.101+1184C>T		intron_variant	Intron 1 of 7		NP_001135774.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC113	ENST00000219299.8	c.101+1184C>T		intron_variant	Intron 1 of 8	1	NM_014157.4	ENSP00000219299.4

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21925 AN: 152148 Hom.: 2091 Cov.: 33

Gnomad AFR AF: 0.0465

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.144 AC: 21929 AN: 152266 Hom.: 2090 Cov.: 33 AF XY: 0.150 AC XY: 11144 AN XY: 74436

Gnomad4 AFR AF: 0.0463

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.151

Alfa AF: 0.148 Hom.: 1016

Bravo AF: 0.148

Asia WGS AF: 0.285 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.63

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: rs1974876; hg19: chr16-58285203;