Variant 10-104132169-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_025145.7(CFAP43):c.4624C>G(p.Leu1542Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.008 in 1,603,012 control chromosomes in the GnomAD database, including 72 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 Likely benign (★★).

Frequency

Genomes: 𝑓 0.0069 ( 14 hom., cov: 32)

Exomes 𝑓: 0.0081 ( 58 hom. )

Consequence

CFAP43
NM_025145.7 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.209

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0041635334).

BP6

Variant 10-104132169-G-C is Benign according to our data. Variant chr10-104132169-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 709932.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00685 (1042/152012) while in subpopulation NFE AF= 0.0104 (706/67982). AF 95% confidence interval is 0.00975. There are 14 homozygotes in gnomad4. There are 544 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 14 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP43	NM_025145.7 linkuse as main transcript	c.4624C>G	p.Leu1542Val	missense_variant	36/38	ENST00000357060.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP43	ENST00000357060.8 linkuse as main transcript	c.4624C>G	p.Leu1542Val	missense_variant	36/38	1	NM_025145.7	P1	Q8NDM7-1
CFAP43	ENST00000434629.5 linkuse as main transcript	c.2620C>G	p.Leu874Val	missense_variant	21/23	1
CFAP43	ENST00000457071.5 linkuse as main transcript	c.1171C>G	p.Leu391Val	missense_variant	10/12	2

Frequencies

GnomAD3 genomes

AF:

0.00687

AC:

1043

AN:

151894

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00152

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00302

Gnomad ASJ

AF:

0.00576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.0185

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0104

Gnomad OTH

AF:

0.00480

GnomAD3 exomes

AF:

0.00608

AC:

1478

AN:

242960

Hom.:

AF XY:

0.00609

AC XY:

798

AN XY:

131136

show subpopulations

Gnomad AFR exome

AF:

0.00131

Gnomad AMR exome

AF:

0.00176

Gnomad ASJ exome

AF:

0.00404

Gnomad EAS exome

AF:

0.0000558

Gnomad SAS exome

AF:

0.00139

Gnomad FIN exome

AF:

0.0149

Gnomad NFE exome

AF:

0.00869

Gnomad OTH exome

AF:

0.00585

GnomAD4 exome

AF:

0.00812

AC:

11781

AN:

1451000

Hom.:

Cov.:

AF XY:

0.00799

AC XY:

5767

AN XY:

721348

show subpopulations

Gnomad4 AFR exome

AF:

0.00118

Gnomad4 AMR exome

AF:

0.00189

Gnomad4 ASJ exome

AF:

0.00382

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00120

Gnomad4 FIN exome

AF:

0.0144

Gnomad4 NFE exome

AF:

0.00926

Gnomad4 OTH exome

AF:

0.00699

GnomAD4 genome

AF:

0.00685

AC:

1042

AN:

152012

Hom.:

Cov.:

AF XY:

0.00732

AC XY:

544

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.00152

Gnomad4 AMR

AF:

0.00295

Gnomad4 ASJ

AF:

0.00576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000416

Gnomad4 FIN

AF:

0.0185

Gnomad4 NFE

AF:

0.0104

Gnomad4 OTH

AF:

0.00475

Alfa

AF:

0.00950

Hom.:

Bravo

AF:

0.00486

TwinsUK

AF:

0.00863

AC:

ALSPAC

AF:

0.00908

AC:

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00978

AC:

ExAC

AF:

0.00589

AC:

715

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2024	CFAP43: BP4, BS2 -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.68

CADD

Benign

1.6

DANN

Benign

0.79

DEOGEN2

Benign

0.039

Eigen

Benign

-0.91

Eigen_PC

Benign

-0.87

FATHMM_MKL

Benign

0.049

LIST_S2

Benign

0.59

MetaRNN

Benign

0.0042

MetaSVM

Benign

-0.96

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.92

REVEL

Benign

0.078

Sift

Benign

0.53

Sift4G

Benign

0.54

Polyphen

0.016

Vest4

0.059

MVP

0.17

MPC

0.14

ClinPred

0.0012

GERP RS

1.6

Varity_R

0.055

gMVP

0.11

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