Variant 18-50251802-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_145020.5(CFAP53):c.474-18T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 1,606,260 control chromosomes in the GnomAD database, including 118,020 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7959 hom., cov: 33)

Exomes 𝑓: 0.38 ( 110061 hom. )

Consequence

CFAP53
NM_145020.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 2.28

Variant links:

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]

CFAP53 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 18-50251802-A-G is Benign according to our data. Variant chr18-50251802-A-G is described in ClinVar as [Benign]. Clinvar id is 262553.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-50251802-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP53	NM_145020.5 linkuse as main transcript	c.474-18T>C		intron_variant		ENST00000398545.5	NP_659457.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP53	ENST00000398545.5 linkuse as main transcript	c.474-18T>C		intron_variant		1	NM_145020.5	ENSP00000381553	P1

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45430

AN:

152006

Hom.:

7961

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.415

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.370

Gnomad EAS

AF:

0.0581

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.426

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.402

Gnomad OTH

AF:

0.325

GnomAD3 exomes

AF:

0.313

AC:

76977

AN:

246316

Hom.:

14069

AF XY:

0.321

AC XY:

42913

AN XY:

133766

show subpopulations

Gnomad AFR exome

AF:

0.137

Gnomad AMR exome

AF:

0.180

Gnomad ASJ exome

AF:

0.348

Gnomad EAS exome

AF:

0.0587

Gnomad SAS exome

AF:

0.270

Gnomad FIN exome

AF:

0.425

Gnomad NFE exome

AF:

0.403

Gnomad OTH exome

AF:

0.355

GnomAD4 exome

AF:

0.378

AC:

549154

AN:

1454136

Hom.:

110061

Cov.:

AF XY:

0.376

AC XY:

271984

AN XY:

722980

show subpopulations

Gnomad4 AFR exome

AF:

0.127

Gnomad4 AMR exome

AF:

0.190

Gnomad4 ASJ exome

AF:

0.352

Gnomad4 EAS exome

AF:

0.0515

Gnomad4 SAS exome

AF:

0.276

Gnomad4 FIN exome

AF:

0.425

Gnomad4 NFE exome

AF:

0.412

Gnomad4 OTH exome

AF:

0.351

GnomAD4 genome

AF:

0.299

AC:

45425

AN:

152124

Hom.:

7959

Cov.:

AF XY:

0.297

AC XY:

22069

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.248

Gnomad4 ASJ

AF:

0.370

Gnomad4 EAS

AF:

0.0581

Gnomad4 SAS

AF:

0.262

Gnomad4 FIN

AF:

0.426

Gnomad4 NFE

AF:

0.402

Gnomad4 OTH

AF:

0.321

Alfa

AF:

0.346

Hom.:

1811

Bravo

AF:

0.277

Asia WGS

AF:

0.158

AC:

550

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Heterotaxy, visceral, 6, autosomal

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.8

DANN

Benign

0.62

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over