6-87418370-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001031743.3(CFAP206):​c.794C>T​(p.Ala265Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,940 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000053 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000082 ( 0 hom. )

Consequence

CFAP206
NM_001031743.3 missense

Scores

6
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.44
Variant links:
Genes affected
CFAP206 (HGNC:21405): (cilia and flagella associated protein 206) Predicted to be involved in regulation of cilium beat frequency; regulation of flagellated sperm motility; and sperm axoneme assembly. Predicted to be located in motile cilium. Predicted to be part of radial spoke. Predicted to be active in axoneme and ciliary basal body. Predicted to colocalize with A axonemal microtubule. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CFAP206NM_001031743.3 linkc.794C>T p.Ala265Val missense_variant Exon 7 of 13 ENST00000369562.9 NP_001026913.1 Q8IYR0Q8N771

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CFAP206ENST00000369562.9 linkc.794C>T p.Ala265Val missense_variant Exon 7 of 13 1 NM_001031743.3 ENSP00000358575.4 Q8IYR0
ENSG00000213204ENST00000507897.5 linkn.794C>T non_coding_transcript_exon_variant Exon 7 of 16 2 ENSP00000426769.1

Frequencies

GnomAD3 genomes
AF:
0.0000526
AC:
8
AN:
152058
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.0000159
AC:
4
AN:
251444
Hom.:
0
AF XY:
0.0000147
AC XY:
2
AN XY:
135906
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000879
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000821
AC:
12
AN:
1461882
Hom.:
0
Cov.:
31
AF XY:
0.0000110
AC XY:
8
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000348
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000450
Gnomad4 OTH exome
AF:
0.0000497
GnomAD4 genome
AF:
0.0000526
AC:
8
AN:
152058
Hom.:
0
Cov.:
31
AF XY:
0.0000404
AC XY:
3
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.000121
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.000478
Bravo
AF:
0.0000453
ExAC
AF:
0.0000165
AC:
2
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Oct 27, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.794C>T (p.A265V) alteration is located in exon 7 (coding exon 6) of the CFAP206 gene. This alteration results from a C to T substitution at nucleotide position 794, causing the alanine (A) at amino acid position 265 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.23
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.21
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.24
T
Eigen
Uncertain
0.31
Eigen_PC
Uncertain
0.29
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Uncertain
0.87
D
M_CAP
Benign
0.024
T
MetaRNN
Uncertain
0.43
T
MetaSVM
Benign
-1.1
T
PROVEAN
Benign
-1.4
N
REVEL
Benign
0.16
Sift
Benign
0.097
T
Sift4G
Benign
0.11
T
Polyphen
0.94
P
Vest4
0.53
MutPred
0.63
Gain of methylation at K263 (P = 0.0989);
MVP
0.22
MPC
0.17
ClinPred
0.56
D
GERP RS
5.2
Varity_R
0.26
gMVP
0.55

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.

Other links and lift over

dbSNP: rs750840329; hg19: chr6-88128088; COSMIC: COSV51534041; COSMIC: COSV51534041; API