Variant chr12-113149862-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001144872.3(CFAP73):c.5C>T(p.Ala2Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00446 in 1,551,280 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0030 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0046 ( 20 hom. )

Consequence

CFAP73
NM_001144872.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.766

Variant links:

Genes affected

CFAP73 (HGNC:37100): (cilia and flagella associated protein 73) Predicted to enable dynein complex binding activity. Predicted to be involved in cilium movement and inner dynein arm assembly. Predicted to be located in axonemal outer doublet and motile cilium. [provided by Alliance of Genome Resources, Apr 2022]

CFAP73 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0068102777).

BP6

Variant 12-113149862-C-T is Benign according to our data. Variant chr12-113149862-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2643350.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 20 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP73	NM_001144872.3 linkuse as main transcript	c.5C>T	p.Ala2Val	missense_variant	1/8	ENST00000335621.11	NP_001138344.1	A6NFT4
CFAP73	XM_011538327.3 linkuse as main transcript	c.5C>T	p.Ala2Val	missense_variant	1/7		XP_011536629.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP73	ENST00000335621.11 linkuse as main transcript	c.5C>T	p.Ala2Val	missense_variant	1/8	5	NM_001144872.3	ENSP00000333915.6		A6NFT4

Frequencies

GnomAD3 genomes

AF:

0.00302

AC:

459

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000869

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00124

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00207

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00519

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00324

AC:

499

AN:

154028

Hom.:

AF XY:

0.00312

AC XY:

255

AN XY:

81736

show subpopulations

Gnomad AFR exome

AF:

0.000505

Gnomad AMR exome

AF:

0.00174

Gnomad ASJ exome

AF:

0.00731

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00149

Gnomad FIN exome

AF:

0.00223

Gnomad NFE exome

AF:

0.00519

Gnomad OTH exome

AF:

0.00277

GnomAD4 exome

AF:

0.00461

AC:

6454

AN:

1398988

Hom.:

Cov.:

AF XY:

0.00455

AC XY:

3139

AN XY:

690028

show subpopulations

Gnomad4 AFR exome

AF:

0.000855

Gnomad4 AMR exome

AF:

0.00168

Gnomad4 ASJ exome

AF:

0.00644

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00148

Gnomad4 FIN exome

AF:

0.00211

Gnomad4 NFE exome

AF:

0.00529

Gnomad4 OTH exome

AF:

0.00454

GnomAD4 genome

AF:

0.00301

AC:

458

AN:

152292

Hom.:

Cov.:

AF XY:

0.00283

AC XY:

211

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.000866

Gnomad4 AMR

AF:

0.00124

Gnomad4 ASJ

AF:

0.00605

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00207

Gnomad4 NFE

AF:

0.00518

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00472

Hom.:

Bravo

AF:

0.00309

TwinsUK

AF:

0.00674

AC:

ALSPAC

AF:

0.00467

AC:

ESP6500AA

AF:

0.00145

AC:

ESP6500EA

AF:

0.00377

AC:

ExAC

AF:

0.00270

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

CFAP73: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.55

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.043

Eigen

Benign

-0.65

Eigen_PC

Benign

-0.81

FATHMM_MKL

Benign

0.061

LIST_S2

Benign

0.58

M_CAP

Benign

0.012

MetaRNN

Benign

0.0068

MetaSVM

Benign

-1.0

PrimateAI

Uncertain

0.49

PROVEAN

Benign

-1.9

REVEL

Benign

0.11

Sift

Benign

0.044

Sift4G

Uncertain

0.048

Polyphen

0.96

Vest4

0.20

MVP

0.076

ClinPred

0.021

GERP RS

0.32

Varity_R

0.045

gMVP

0.33

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