12-9681030-AGC-CGG

Variant names:

• chr12-9681030-AGC-CGG
• NM_013269.6:c.169_171delAGCinsCGG
• CLEC2D p.Ser57Arg

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_013269.6(CLEC2D):​c.169_171delAGCinsCGG​(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. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013269.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC2D	NM_013269.6	MANE Select	c.169_171delAGCinsCGG	p.Ser57Arg	missense splice_region	N/A	NP_037401.1	Q9UHP7-1
	CLEC2D	NM_001004419.5		c.169_171delAGCinsCGG	p.Ser57Arg	missense splice_region	N/A	NP_001004419.1	Q9UHP7-3
	CLEC2D	NM_001197318.3		c.169_171delAGCinsCGG	p.Ser57Arg	missense splice_region	N/A	NP_001184247.1	Q9UHP7-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC2D	ENST00000290855.11	TSL:1 MANE Select	c.169_171delAGCinsCGG	p.Ser57Arg	missense splice_region	N/A	ENSP00000290855.6	Q9UHP7-1
	CLEC2D	ENST00000261340.11	TSL:1	c.169_171delAGCinsCGG	p.Ser57Arg	missense splice_region	N/A	ENSP00000261340.7	Q9UHP7-3
	CLEC2D	ENST00000430909.5	TSL:1	c.106_108delAGCinsCGG	p.Ser36Arg	missense splice_region	N/A	ENSP00000413045.1	A0A0C4DG81

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.027

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr12-9833626;