rs2073961090

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_198491.3(CIBAR2):​c.629A>G​(p.Tyr210Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000688 in 1,454,152 control chromosomes in the GnomAD database, with no homozygous occurrence. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000069 ( 0 hom. )

Consequence

CIBAR2
NM_198491.3 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.36

Publications

0 publications found
Variant links:
Genes affected
CIBAR2 (HGNC:24781): (CBY1 interacting BAR domain containing 2) Predicted to be involved in cilium assembly. Predicted to be located in centriole and cytoplasm. Predicted to be active in ciliary basal body and ciliary transition zone. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 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
CIBAR2NM_198491.3 linkc.629A>G p.Tyr210Cys missense_variant Exon 7 of 9 ENST00000539556.6 NP_940893.1 Q6ZTR7A0A1X7SC74
CIBAR2NM_001366920.1 linkc.629A>G p.Tyr210Cys missense_variant Exon 7 of 9 NP_001353849.1
CIBAR2XM_011523063.2 linkc.629A>G p.Tyr210Cys missense_variant Exon 7 of 10 XP_011521365.1 Q6ZTR7A0A1X7SC74
CIBAR2XM_017023198.2 linkc.629A>G p.Tyr210Cys missense_variant Exon 7 of 10 XP_016878687.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CIBAR2ENST00000539556.6 linkc.629A>G p.Tyr210Cys missense_variant Exon 7 of 9 5 NM_198491.3 ENSP00000443411.1 A0A1X7SC74
CIBAR2ENST00000618669.3 linkc.344A>G p.Tyr115Cys missense_variant Exon 5 of 7 5 ENSP00000478373.1 A0A087WU51

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000688
AC:
10
AN:
1454152
Hom.:
0
Cov.:
28
AF XY:
0.00000276
AC XY:
2
AN XY:
724038
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33318
American (AMR)
AF:
0.00
AC:
0
AN:
44712
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26094
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39666
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86102
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53408
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5756
European-Non Finnish (NFE)
AF:
0.00000905
AC:
10
AN:
1104946
Other (OTH)
AF:
0.00
AC:
0
AN:
60150
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.430
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
May 17, 2025
Ambry Genetics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The c.629A>G (p.Y210C) alteration is located in exon 7 (coding exon 7) of the FAM92B gene. This alteration results from a A to G substitution at nucleotide position 629, causing the tyrosine (Y) at amino acid position 210 to be replaced by a cysteine (C). 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
Uncertain
0.37
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.40
CADD
Benign
18
DANN
Benign
0.91
DEOGEN2
Benign
0.0099
.;T
Eigen
Benign
-0.40
Eigen_PC
Benign
-0.38
FATHMM_MKL
Benign
0.29
N
LIST_S2
Benign
0.76
T;T
M_CAP
Benign
0.021
T
MetaRNN
Uncertain
0.59
D;D
MetaSVM
Benign
-0.98
T
MutationAssessor
Benign
2.0
.;M
PhyloP100
2.4
PrimateAI
Benign
0.46
T
PROVEAN
Benign
-1.8
N;.
REVEL
Benign
0.13
Sift
Benign
0.046
D;.
Sift4G
Benign
0.066
T;T
Polyphen
0.11
.;B
Vest4
0.67
MutPred
0.46
Gain of methylation at K209 (P = 0.0159);Gain of methylation at K209 (P = 0.0159);
MVP
0.27
MPC
0.077
ClinPred
0.32
T
GERP RS
4.6
Varity_R
0.10
gMVP
0.29
Mutation Taster
=89/11
polymorphism

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

Other links and lift over

dbSNP: rs2073961090; hg19: chr16-85135842; API