rs121908256

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM2PM5BP4_Strong

The ENST00000310942.9(CBX2):​c.1328G>A​(p.Arg443His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000932 in 1,609,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R443P) has been classified as Pathogenic.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000096 ( 0 hom. )

Consequence

CBX2
ENST00000310942.9 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.714
Variant links:
Genes affected
CBX2 (HGNC:1552): (chromobox 2) This gene encodes a component of the polycomb multiprotein complex, which is required to maintain the transcriptionally repressive state of many genes throughout development via chromatin remodeling and modification of histones. Disruption of this gene in mice results in male-to-female gonadal sex reversal. Mutations in this gene are also associated with gonadal dysgenesis in humans. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Mar 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr17-79784771-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 6827.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
Computational evidence support a benign effect (MetaRNN=0.027329206).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CBX2NM_005189.3 linkuse as main transcriptc.1328G>A p.Arg443His missense_variant 5/5 ENST00000310942.9 NP_005180.1
CBX2XM_011525382.2 linkuse as main transcriptc.1328G>A p.Arg443His missense_variant 5/6 XP_011523684.1
CBX2XM_011525383.3 linkuse as main transcriptc.1073G>A p.Arg358His missense_variant 5/6 XP_011523685.1
CBX2XM_047436946.1 linkuse as main transcriptc.1073G>A p.Arg358His missense_variant 4/5 XP_047292902.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CBX2ENST00000310942.9 linkuse as main transcriptc.1328G>A p.Arg443His missense_variant 5/51 NM_005189.3 ENSP00000308750 P1Q14781-1

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152182
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000208
AC:
5
AN:
239942
Hom.:
0
AF XY:
0.0000229
AC XY:
3
AN XY:
130720
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000559
Gnomad SAS exome
AF:
0.0000333
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000280
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000960
AC:
14
AN:
1457748
Hom.:
0
Cov.:
34
AF XY:
0.0000138
AC XY:
10
AN XY:
724872
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000253
Gnomad4 SAS exome
AF:
0.0000233
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000810
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152182
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.0000241
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:
0.00
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.0000495
AC:
6
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.059
BayesDel_addAF
Benign
-0.30
T
BayesDel_noAF
Benign
-0.68
CADD
Benign
0.52
DANN
Benign
0.39
DEOGEN2
Benign
0.048
T
Eigen
Benign
-1.5
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.058
N
LIST_S2
Benign
0.66
T
M_CAP
Benign
0.0062
T
MetaRNN
Benign
0.027
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-0.77
N
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.24
T
PROVEAN
Benign
1.2
N
REVEL
Benign
0.074
Sift
Benign
1.0
T
Sift4G
Benign
0.59
T
Polyphen
0.0010
B
Vest4
0.039
MutPred
0.15
Loss of MoRF binding (P = 0.0373);
MVP
0.19
MPC
0.044
ClinPred
0.0086
T
GERP RS
-5.7
Varity_R
0.021
gMVP
0.13

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: rs121908256; hg19: chr17-77758570; API