Variant 1-43156263-ACT-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001101376.3(CFAP144):c.358_359del(p.Leu120ValfsTer4) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000413 in 1,613,950 control chromosomes in the GnomAD database, including 6 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0021 ( 1 hom., cov: 32)

Exomes 𝑓: 0.00024 ( 5 hom. )

Consequence

CFAP144
NM_001101376.3 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.996

Variant links:

Genes affected

CFAP144 (HGNC:34347): (cilia and flagella associated protein 144) Predicted to be located in centrosome and ciliary basal body. Predicted to be active in ciliary base. [provided by Alliance of Genome Resources, Apr 2022]

CFAP144 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 1-43156263-ACT-A is Benign according to our data. Variant chr1-43156263-ACT-A is described in ClinVar as [Benign]. Clinvar id is 783936.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CFAP144	NM_001101376.3 linkuse as main transcript	c.358_359del	p.Leu120ValfsTer4	frameshift_variant	4/4	ENST00000335282.5
CFAP144	XM_005270875.6 linkuse as main transcript	c.406_407del	p.Leu136ValfsTer4	frameshift_variant	4/4
CFAP144	XM_005270876.5 linkuse as main transcript	c.322_323del	p.Leu108ValfsTer4	frameshift_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP144	ENST00000335282.5 linkuse as main transcript	c.358_359del	p.Leu120ValfsTer4	frameshift_variant	4/4	2	NM_001101376.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00208

AC:

316

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00703

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00137

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.000594

AC:

148

AN:

249262

Hom.:

AF XY:

0.000436

AC XY:

AN XY:

135226

show subpopulations

Gnomad AFR exome

AF:

0.00827

Gnomad AMR exome

AF:

0.000232

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000163

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000177

Gnomad OTH exome

AF:

0.000826

GnomAD4 exome

AF:

0.000237

AC:

347

AN:

1461710

Hom.:

AF XY:

0.000195

AC XY:

142

AN XY:

727138

show subpopulations

Gnomad4 AFR exome

AF:

0.00833

Gnomad4 AMR exome

AF:

0.000291

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000128

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000270

Gnomad4 OTH exome

AF:

0.000679

GnomAD4 genome

AF:

0.00210

AC:

319

AN:

152240

Hom.:

Cov.:

AF XY:

0.00214

AC XY:

159

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.00708

Gnomad4 AMR

AF:

0.00137

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000294

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.000995

Hom.:

Bravo

AF:

0.00243

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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