rs955578545

Variant summary

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

The NM_001802.2(CDR2):​c.982G>C​(p.Glu328Gln) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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. E328K) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

CDR2
NM_001802.2 missense

Scores

1
5
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.46
Variant links:
Genes affected
CDR2 (HGNC:1799): (cerebellar degeneration related protein 2) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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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
CDR2NM_001802.2 linkc.982G>C p.Glu328Gln missense_variant Exon 5 of 5 ENST00000268383.7 NP_001793.1 Q01850
CDR2XM_024450143.2 linkc.757G>C p.Glu253Gln missense_variant Exon 4 of 4 XP_024305911.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CDR2ENST00000268383.7 linkc.982G>C p.Glu328Gln missense_variant Exon 5 of 5 1 NM_001802.2 ENSP00000268383.2 Q01850
CDR2ENST00000564542.5 linkc.*127G>C downstream_gene_variant 5 ENSP00000457432.1 H3BU23

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.43
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.29
T
Eigen
Uncertain
0.42
Eigen_PC
Uncertain
0.43
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Benign
0.83
T
M_CAP
Benign
0.033
D
MetaRNN
Uncertain
0.72
D
MetaSVM
Benign
-0.76
T
MutationAssessor
Benign
1.4
L
PrimateAI
Uncertain
0.50
T
PROVEAN
Benign
-0.89
N
REVEL
Benign
0.17
Sift
Benign
0.21
T
Sift4G
Benign
0.35
T
Polyphen
0.99
D
Vest4
0.61
MutPred
0.27
Gain of MoRF binding (P = 0.0266);
MVP
0.86
MPC
0.78
ClinPred
0.81
D
GERP RS
4.8
Varity_R
0.16

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: rs955578545; hg19: chr16-22358669; API