rs3764021

Positions:

• chr12-9681032-C-G
• chr12-9681032-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_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: Splicing: ADA: 0.0002127
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

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]

ACMG classification

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
CLEC2D	NM_013269.6	c.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
CLEC2D	ENST00000290855.11	c.171C>G	p.Ser57Arg	missense_variant, splice_region_variant	2/5	1	NM_013269.6	P2

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

Other links and lift over

dbSNP: rs3764021; hg19: chr12-9833628;