19-54594462-CC-TA

Variant names:

• chr19-54594462-CC-TA
• NM_006863.4:c.56_57delCCinsTA
• LILRA1 p.Thr19Ile

Variant summary

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

The NM_006863.4(LILRA1):​c.56_57delCCinsTA​(p.Thr19Ile) 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 37)
• Consequence: LILRA1 NM_006863.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 0 publications found

Genes affected

LILRA1 (HGNC:6602): (leukocyte immunoglobulin like receptor A1) This gene encodes an activating member of the leukocyte immunoglobulin-like receptor (LIR) family, which is found in a gene cluster at chromosomal region 19q13.4. The encoded protein is predominantly expressed in B cells, interacts with major histocompatibility complex class I ligands, and contributes to the regulation of immune responses. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006863.4. 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
	LILRA1	NM_006863.4	MANE Select	c.56_57delCCinsTA	p.Thr19Ile	missense	N/A	NP_006854.1	O75019-1
	LILRA1	NM_001278319.1		c.56_57delCCinsTA	p.Thr19Ile	missense	N/A	NP_001265248.1	O75019
	LILRA1	NM_001278318.2		c.56_57delCCinsTA	p.Thr19Ile	missense	N/A	NP_001265247.1	O75019-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRA1	ENST00000251372.8	TSL:1 MANE Select	c.56_57delCCinsTA	p.Thr19Ile	missense	N/A	ENSP00000251372.3	O75019-1
	LILRA1	ENST00000453777.1	TSL:1	c.56_57delCCinsTA	p.Thr19Ile	missense	N/A	ENSP00000413715.1	O75019-2
	LILRA1	ENST00000473156.5	TSL:1	n.222_223delCCinsTA		non_coding_transcript_exon	Exon 2 of 9

Frequencies

GnomAD3 genomes Cov.: 37

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

GnomAD4 genome Cov.: 37

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.47

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: chr19-55105927;