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10-104140974-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_025145.7(CFAP43):c.4299G>A(p.Gln1433=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0244 in 1,611,616 control chromosomes in the GnomAD database, including 616 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.017 ( 33 hom., cov: 32)
Exomes 𝑓: 0.025 ( 583 hom. )

Consequence

CFAP43
NM_025145.7 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.576
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 10-104140974-C-T is Benign according to our data. Variant chr10-104140974-C-T is described in ClinVar as [Benign]. Clinvar id is 3056592.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.576 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.017 (2583/152296) while in subpopulation NFE AF= 0.0264 (1796/68016). AF 95% confidence interval is 0.0254. There are 33 homozygotes in gnomad4. There are 1225 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 33 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CFAP43NM_025145.7 linkuse as main transcriptc.4299G>A p.Gln1433= synonymous_variant 34/38 ENST00000357060.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CFAP43ENST00000357060.8 linkuse as main transcriptc.4299G>A p.Gln1433= synonymous_variant 34/381 NM_025145.7 P1Q8NDM7-1
CFAP43ENST00000434629.5 linkuse as main transcriptc.2295G>A p.Gln765= synonymous_variant 19/231
CFAP43ENST00000457071.5 linkuse as main transcriptc.846G>A p.Gln282= synonymous_variant 8/122
CFAP43ENST00000479392.1 linkuse as main transcriptn.63G>A non_coding_transcript_exon_variant 2/35

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0170
AC:
2581
AN:
152178
Hom.:
33
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00504
Gnomad AMI
AF:
0.0681
Gnomad AMR
AF:
0.0111
Gnomad ASJ
AF:
0.0101
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0145
Gnomad FIN
AF:
0.0192
Gnomad MID
AF:
0.0190
Gnomad NFE
AF:
0.0264
Gnomad OTH
AF:
0.0144
GnomAD3 exomes
AF:
0.0169
AC:
4188
AN:
247926
Hom.:
61
AF XY:
0.0177
AC XY:
2365
AN XY:
133974
show subpopulations
Gnomad AFR exome
AF:
0.00547
Gnomad AMR exome
AF:
0.00701
Gnomad ASJ exome
AF:
0.00849
Gnomad EAS exome
AF:
0.0000549
Gnomad SAS exome
AF:
0.0137
Gnomad FIN exome
AF:
0.0233
Gnomad NFE exome
AF:
0.0245
Gnomad OTH exome
AF:
0.0190
GnomAD4 exome
AF:
0.0252
AC:
36744
AN:
1459320
Hom.:
583
Cov.:
31
AF XY:
0.0246
AC XY:
17863
AN XY:
725816
show subpopulations
Gnomad4 AFR exome
AF:
0.00491
Gnomad4 AMR exome
AF:
0.00725
Gnomad4 ASJ exome
AF:
0.00828
Gnomad4 EAS exome
AF:
0.0000505
Gnomad4 SAS exome
AF:
0.0147
Gnomad4 FIN exome
AF:
0.0228
Gnomad4 NFE exome
AF:
0.0289
Gnomad4 OTH exome
AF:
0.0232
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0170
AC:
2583
AN:
152296
Hom.:
33
Cov.:
32
AF XY:
0.0165
AC XY:
1225
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.00503
Gnomad4 AMR
AF:
0.0110
Gnomad4 ASJ
AF:
0.0101
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0147
Gnomad4 FIN
AF:
0.0192
Gnomad4 NFE
AF:
0.0264
Gnomad4 OTH
AF:
0.0142
Alfa
AF:
0.0224
Hom.:
34
Bravo
AF:
0.0162
Asia WGS
AF:
0.00260
AC:
9
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

CFAP43-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesJul 10, 2019This 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
BayesDel_noAF
Benign
-0.43
Cadd
Benign
8.3
Dann
Benign
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
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.

Other links and lift over

dbSNP: rs45618238; hg19: chr10-105900732; API