rs768360

Positions:

• chr18-50237703-A-G

Variant summary

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

The NM_145020.5(CFAP53):​c.1316+900T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,666 control chromosomes in the GnomAD database, including 8,546 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 0.33 (8546 hom., cov: 30)
• Consequence: CFAP53 NM_145020.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871

Genes affected

CFAP53 (HGNC:26530): (cilia and flagella associated protein 53) This gene belongs to the CFAP53 family. It was found to be differentially expressed by the ciliated cells of frog epidermis and in skin fibroblasts from human. Mutations in this gene are associated with visceral heterotaxy-6, which implicates this gene in determination of left-right asymmetric patterning. [provided by RefSeq, Aug 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP53	NM_145020.5	c.1316+900T>C		intron_variant		ENST00000398545.5	NP_659457.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP53	ENST00000398545.5	c.1316+900T>C		intron_variant		1	NM_145020.5	ENSP00000381553.3

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49753 AN: 151548 Hom.: 8530 Cov.: 30

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.328 AC: 49809 AN: 151666 Hom.: 8546 Cov.: 30 AF XY: 0.326 AC XY: 24153 AN XY: 74048

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.300

Alfa AF: 0.313 Hom.: 1295

Bravo AF: 0.327

Asia WGS AF: 0.300 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.90
DANN	Benign	0.30

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: rs768360; hg19: chr18-47764073;