19-54510541-CT-TC

Variant names:

• chr19-54510541-CT-TC
• NM_002288.6:c.431_432delCTinsTC
• LAIR2 p.Thr144Ile

Variant summary

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

The NM_002288.6(LAIR2):​c.431_432delCTinsTC​(p.Thr144Ile) variant causes a missense 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T144S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 30)
• Consequence: LAIR2 NM_002288.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 0 publications found

Genes affected

LAIR2 (HGNC:6478): (leukocyte associated immunoglobulin like receptor 2) The protein encoded by this gene is a member of the immunoglobulin superfamily. It was identified by its similarity to leukocyte-associated immunoglobulin-like receptor 1, a membrane-bound receptor that modulates innate immune response. The protein encoded by this locus is a soluble receptor that may play roles in both inhibition of collagen-induced platelet aggregation and vessel formation during placental implantation. This gene maps to a region of 19q13.4, termed the leukocyte receptor cluster, which contains 29 genes in the immunoglobulin superfamily. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Sep 2013]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002288.6. 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
	LAIR2	NM_002288.6	MANE Select	c.431_432delCTinsTC	p.Thr144Ile	missense	N/A	NP_002279.2
	LAIR2	NM_021270.5		c.380_381delCTinsTC	p.Thr127Ile	missense	N/A	NP_067154.1	Q6ISS4-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAIR2	ENST00000301202.7	TSL:1 MANE Select	c.431_432delCTinsTC	p.Thr144Ile	missense	N/A	ENSP00000301202.2	Q6ISS4-1
	LAIR2	ENST00000351841.2	TSL:1	c.380_381delCTinsTC	p.Thr127Ile	missense	N/A	ENSP00000301203.2	Q6ISS4-2
	LAIR2	ENST00000956664.1		c.395_396delCTinsTC	p.Thr132Ile	missense	N/A	ENSP00000626723.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.022

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: chr19-55021751;