chr16-30353471-C-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_006110.3(CD2BP2):​c.705G>C​(p.Gln235His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,614,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000062 ( 0 hom. )

Consequence

CD2BP2
NM_006110.3 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.01
Variant links:
Genes affected
CD2BP2 (HGNC:1656): (CD2 cytoplasmic tail binding protein 2) This gene encodes a bi-functional protein. In the cytoplasm, the encoded protein binds the cytoplasmic tail of human surface antigen CD2 via its C-terminal GYF domain, and regulate CD2-triggered T lymphocyte activation. In the nucleus, this protein is a component of the U5 small nuclear ribonucleoprotein complex and is involved in RNA splicing. A pseudogene has been identified on chromosome 7. Alternative splicing results in multiple transcript variants but their biological validity has not been determined. [provided by RefSeq, Nov 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 10 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CD2BP2NM_006110.3 linkc.705G>C p.Gln235His missense_variant Exon 5 of 7 ENST00000305596.8 NP_006101.1 O95400A0A024QZC1
CD2BP2NM_001243646.2 linkc.705G>C p.Gln235His missense_variant Exon 4 of 6 NP_001230575.1 O95400A0A024QZC1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CD2BP2ENST00000305596.8 linkc.705G>C p.Gln235His missense_variant Exon 5 of 7 1 NM_006110.3 ENSP00000304903.3 O95400
CD2BP2ENST00000569466.1 linkc.705G>C p.Gln235His missense_variant Exon 4 of 6 1 ENSP00000456935.1 O95400

Frequencies

GnomAD3 genomes
AF:
0.0000657
AC:
10
AN:
152152
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
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:
0.000118
Gnomad OTH
AF:
0.000480
GnomAD3 exomes
AF:
0.0000716
AC:
18
AN:
251414
Hom.:
0
AF XY:
0.0000736
AC XY:
10
AN XY:
135900
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000260
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000704
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.0000623
AC:
91
AN:
1461838
Hom.:
0
Cov.:
33
AF XY:
0.0000591
AC XY:
43
AN XY:
727218
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000246
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000621
Gnomad4 OTH exome
AF:
0.000182
GnomAD4 genome
AF:
0.0000657
AC:
10
AN:
152270
Hom.:
0
Cov.:
32
AF XY:
0.000107
AC XY:
8
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.000475
Alfa
AF:
0.000226
Hom.:
0
Bravo
AF:
0.0000718
ExAC
AF:
0.0000412
AC:
5
EpiCase
AF:
0.000218
EpiControl
AF:
0.000119

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Feb 13, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.705G>C (p.Q235H) alteration is located in exon 5 (coding exon 4) of the CD2BP2 gene. This alteration results from a G to C substitution at nucleotide position 705, causing the glutamine (Q) at amino acid position 235 to be replaced by a histidine (H). 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
0.11
BayesDel_addAF
Benign
-0.50
T
BayesDel_noAF
Benign
-0.65
CADD
Benign
20
DANN
Benign
0.96
DEOGEN2
Benign
0.0094
T;T
Eigen
Benign
-0.47
Eigen_PC
Benign
-0.39
FATHMM_MKL
Benign
0.42
N
LIST_S2
Benign
0.62
.;T
M_CAP
Benign
0.0068
T
MetaRNN
Benign
0.054
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.2
L;L
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-1.1
N;N
REVEL
Benign
0.024
Sift
Benign
0.071
T;T
Sift4G
Benign
0.070
T;T
Polyphen
0.10
B;B
Vest4
0.098
MutPred
0.42
Loss of MoRF binding (P = 0.1004);Loss of MoRF binding (P = 0.1004);
MVP
0.35
MPC
0.095
ClinPred
0.047
T
GERP RS
2.3
Varity_R
0.081
gMVP
0.46

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.32
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.32
Position offset: -8

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: rs557542579; hg19: chr16-30364792; API