rs3764021

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_013269.6(CLEC2D):​c.171C>G​(p.Ser57Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

CLEC2D
NM_013269.6 missense, splice_region

Scores

2
17
Splicing: ADA: 0.0002127
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.588
Variant links:
Genes affected
CLEC2D (HGNC:14351): (C-type lectin domain family 2 member D) This gene encodes a member of the natural killer cell receptor C-type lectin family. The encoded protein inhibits osteoclast formation and contains a transmembrane domain near the N-terminus as well as the C-type lectin-like extracellular domain. Several alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Oct 2010]

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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;
BP4
Computational evidence support a benign effect (MetaRNN=0.1113247).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CLEC2DNM_013269.6 linkuse as main transcriptc.171C>G p.Ser57Arg missense_variant, splice_region_variant 2/5 ENST00000290855.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CLEC2DENST00000290855.11 linkuse as main transcriptc.171C>G p.Ser57Arg missense_variant, splice_region_variant 2/51 NM_013269.6 P2Q9UHP7-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
20
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.28
BayesDel_addAF
Benign
-0.20
T
BayesDel_noAF
Benign
-0.52
CADD
Benign
0.073
DANN
Uncertain
0.98
DEOGEN2
Benign
0.0097
.;T;.;T;.
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.0052
N
LIST_S2
Benign
0.63
T;T;T;T;T
M_CAP
Benign
0.0017
T
MetaRNN
Benign
0.11
T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.7
L;L;L;.;.
MutationTaster
Benign
1.0
N;N;N;N;N
PrimateAI
Benign
0.37
T
PROVEAN
Uncertain
-2.4
N;N;N;N;N
REVEL
Benign
0.12
Sift
Benign
0.34
T;T;T;T;T
Sift4G
Benign
0.43
T;T;T;T;T
Polyphen
1.0
D;P;D;.;.
Vest4
0.19
MutPred
0.59
Gain of catalytic residue at M52 (P = 0);Gain of catalytic residue at M52 (P = 0);Gain of catalytic residue at M52 (P = 0);.;.;
MVP
0.068
MPC
0.11
ClinPred
0.50
T
GERP RS
-2.4
Varity_R
0.044
gMVP
0.29

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00021
dbscSNV1_RF
Benign
0.11
SpliceAI score (max)
0.040
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: rs3764021; hg19: chr12-9833628; API