Variant chr10-104197956-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_025145.7(CFAP43):c.1178T>C(p.Ile393Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.057 in 1,612,784 control chromosomes in the GnomAD database, including 3,284 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.051 ( 246 hom., cov: 33)

Exomes 𝑓: 0.058 ( 3038 hom. )

Consequence

CFAP43
NM_025145.7 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.883

Variant links:

Genes affected

CFAP43 (HGNC:26684): (cilia and flagella associated protein 43) This gene encodes a member of the cilia- and flagella-associated protein family. [provided by RefSeq, Sep 2016]

CFAP43 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0013535917).

BP6

Variant 10-104197956-A-G is Benign according to our data. Variant chr10-104197956-A-G is described in ClinVar as [Benign]. Clinvar id is 3059847.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP43	NM_025145.7 link	c.1178T>C	p.Ile393Thr	missense_variant	9/38	ENST00000357060.8	NP_079421.5	Q8NDM7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CFAP43	ENST00000357060.8 link	c.1178T>C	p.Ile393Thr	missense_variant	9/38	1	NM_025145.7	ENSP00000349568.3	Q8NDM7-1
CFAP43	ENST00000278064.7 link	c.1181T>C	p.Ile394Thr	missense_variant	9/22	1		ENSP00000278064.3	Q5TA04
CFAP43	ENST00000369720.6 link	c.1181T>C	p.Ile394Thr	missense_variant	9/11	1		ENSP00000358734.2	A0A0C4DFU9

Frequencies

GnomAD3 genomes

AF:

0.0506

AC:

7697

AN:

152192

Hom.:

243

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0424

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0446

Gnomad ASJ

AF:

0.104

Gnomad EAS

AF:

0.103

Gnomad SAS

AF:

0.132

Gnomad FIN

AF:

0.0149

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0505

Gnomad OTH

AF:

0.0532

GnomAD3 exomes

AF:

0.0631

AC:

15848

AN:

251048

Hom.:

699

AF XY:

0.0664

AC XY:

9006

AN XY:

135686

show subpopulations

Gnomad AFR exome

AF:

0.0441

Gnomad AMR exome

AF:

0.0419

Gnomad ASJ exome

AF:

0.112

Gnomad EAS exome

AF:

0.106

Gnomad SAS exome

AF:

0.125

Gnomad FIN exome

AF:

0.0164

Gnomad NFE exome

AF:

0.0537

Gnomad OTH exome

AF:

0.0550

GnomAD4 exome

AF:

0.0577

AC:

84280

AN:

1460474

Hom.:

3038

Cov.:

AF XY:

0.0599

AC XY:

43500

AN XY:

726550

show subpopulations

Gnomad4 AFR exome

AF:

0.0434

Gnomad4 AMR exome

AF:

0.0415

Gnomad4 ASJ exome

AF:

0.117

Gnomad4 EAS exome

AF:

0.0910

Gnomad4 SAS exome

AF:

0.126

Gnomad4 FIN exome

AF:

0.0175

Gnomad4 NFE exome

AF:

0.0523

Gnomad4 OTH exome

AF:

0.0669

GnomAD4 genome

AF:

0.0507

AC:

7720

AN:

152310

Hom.:

246

Cov.:

AF XY:

0.0505

AC XY:

3765

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.0424

Gnomad4 AMR

AF:

0.0446

Gnomad4 ASJ

AF:

0.104

Gnomad4 EAS

AF:

0.103

Gnomad4 SAS

AF:

0.132

Gnomad4 FIN

AF:

0.0149

Gnomad4 NFE

AF:

0.0506

Gnomad4 OTH

AF:

0.0602

Alfa

AF:

0.0575

Hom.:

765

Bravo

AF:

0.0515

TwinsUK

AF:

0.0491

AC:

182

ALSPAC

AF:

0.0576

AC:

222

ESP6500AA

AF:

0.0397

AC:

175

ESP6500EA

AF:

0.0548

AC:

471

ExAC

AF:

0.0640

AC:

7764

Asia WGS

AF:

0.147

AC:

511

AN:

3478

EpiCase

AF:

0.0537

EpiControl

AF:

0.0552

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CFAP43-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 17, 2019

This variant is classified as 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

0.070

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Benign

0.78

DEOGEN2

Benign

0.084

T;T;.

Eigen

Benign

-0.73

Eigen_PC

Benign

-0.67

FATHMM_MKL

Benign

0.14

LIST_S2

Benign

0.44

T;T;T

MetaRNN

Benign

0.0014

T;T;T

MetaSVM

Benign

-1.0

PrimateAI

Benign

0.25

PROVEAN

Benign

-1.8

N;N;N

REVEL

Benign

0.069

Sift

Benign

0.20

T;T;T

Sift4G

Benign

0.31

T;T;T

Polyphen

0.0

B;.;.

Vest4

0.047

MPC

0.17

ClinPred

0.0030

GERP RS

2.2

Varity_R

0.054

gMVP

0.38

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