chr11-102047486-C-T

Variant names:

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_032930.3(CFAP300):c.16C>T(p.Leu6Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00185 in 1,535,916 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0016 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0019 ( 6 hom. )

Consequence

CFAP300
NM_032930.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.270

Variant links:

Genes affected

CFAP300 (HGNC:28188): (cilia and flagella associated protein 300) Predicted to be located in cytoplasm and motile cilium. Implicated in primary ciliary dyskinesia 38. [provided by Alliance of Genome Resources, Apr 2022]

CFAP300 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0030524433).

BP6

Variant 11-102047486-C-T is Benign according to our data. Variant chr11-102047486-C-T is described in ClinVar as [Benign]. Clinvar id is 1681444.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00157 (239/152338) while in subpopulation EAS AF= 0.00213 (11/5168). AF 95% confidence interval is 0.00173. There are 1 homozygotes in gnomad4. There are 112 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP300	NM_032930.3 link	c.16C>T	p.Leu6Phe	missense_variant	Exon 1 of 7	ENST00000434758.7	NP_116319.2	Q9BRQ4-1
CFAP300	NM_001363505.2 link	c.16C>T	p.Leu6Phe	missense_variant	Exon 1 of 6		NP_001350434.1
CFAP300	NM_001195005.2 link	c.16C>T	p.Leu6Phe	missense_variant	Exon 1 of 4		NP_001181934.1	Q7Z2V0
CFAP300	XM_005271713.5 link	c.16C>T	p.Leu6Phe	missense_variant	Exon 1 of 6		XP_005271770.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CFAP300	ENST00000434758.7 link	c.16C>T	p.Leu6Phe	missense_variant	Exon 1 of 7	2	NM_032930.3	ENSP00000414390.2	Q9BRQ4-1
CFAP300	ENST00000534360.1 link	c.16C>T	p.Leu6Phe	missense_variant	Exon 1 of 4	1		ENSP00000435482.1	Q9BRQ4-3
CFAP300	ENST00000530659.1 link	n.19C>T		non_coding_transcript_exon_variant	Exon 1 of 6	1
CFAP300	ENST00000526781.5 link	c.16C>T	p.Leu6Phe	missense_variant	Exon 1 of 6	3		ENSP00000433074.1	E9PM77

Frequencies

GnomAD3 genomes

AF:

0.00157

AC:

239

AN:

152220

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000531

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.00164

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.00165

Gnomad FIN

AF:

0.000848

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00200

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00164

AC:

225

AN:

136836

Hom.:

AF XY:

0.00172

AC XY:

128

AN XY:

74320

show subpopulations

Gnomad AFR exome

AF:

0.000466

Gnomad AMR exome

AF:

0.000776

Gnomad ASJ exome

AF:

0.000241

Gnomad EAS exome

AF:

0.00276

Gnomad SAS exome

AF:

0.00204

Gnomad FIN exome

AF:

0.00111

Gnomad NFE exome

AF:

0.00207

Gnomad OTH exome

AF:

0.00144

GnomAD4 exome

AF:

0.00188

AC:

2602

AN:

1383578

Hom.:

Cov.:

AF XY:

0.00191

AC XY:

1303

AN XY:

682758

show subpopulations

Gnomad4 AFR exome

AF:

0.000317

Gnomad4 AMR exome

AF:

0.000700

Gnomad4 ASJ exome

AF:

0.000159

Gnomad4 EAS exome

AF:

0.00129

Gnomad4 SAS exome

AF:

0.00206

Gnomad4 FIN exome

AF:

0.000797

Gnomad4 NFE exome

AF:

0.00205

Gnomad4 OTH exome

AF:

0.00199

GnomAD4 genome

AF:

0.00157

AC:

239

AN:

152338

Hom.:

Cov.:

AF XY:

0.00150

AC XY:

112

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.000529

Gnomad4 AMR

AF:

0.00163

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00213

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.000848

Gnomad4 NFE

AF:

0.00200

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00201

Hom.:

Bravo

AF:

0.00142

TwinsUK

AF:

0.00243

AC:

ALSPAC

AF:

0.00208

AC:

ExAC

AF:

0.000712

AC:

Asia WGS

AF:

0.00693

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

CFAP300-related disorder

Benign:1

Jun 03, 2022

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.73

CADD

Benign

5.6

DANN

Benign

0.80

DEOGEN2

Benign

0.020

T;.;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.023

LIST_S2

Benign

0.41

T;T;T

M_CAP

Benign

0.0034

MetaRNN

Benign

0.0031

T;T;T

MetaSVM

Benign

-1.0

PROVEAN

Benign

-0.24

N;N;N

REVEL

Benign

0.021

Sift

Benign

0.58

T;T;T

Sift4G

Benign

0.55

T;T;T

Polyphen

0.59

P;.;.

Vest4

0.053

MVP

0.040

MPC

0.044

ClinPred

0.0017

GERP RS

1.7

Varity_R

0.043

gMVP

0.19

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