chr19-54594932-C-T

Variant names:

• chr19-54594932-C-T
• NM_006863.4:c.338C>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_006863.4(LILRA1):​c.338C>T​(p.Pro113Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: LILRA1 NM_006863.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.769
• 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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.338C>T	p.Pro113Leu	missense	Exon 4 of 10	NP_006854.1	O75019-1
	LILRA1	NM_001278319.1		c.338C>T	p.Pro113Leu	missense	Exon 3 of 7	NP_001265248.1	O75019
	LILRA1	NM_001278318.2		c.338C>T	p.Pro113Leu	missense	Exon 4 of 8	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.338C>T	p.Pro113Leu	missense	Exon 4 of 10	ENSP00000251372.3	O75019-1
	LILRA1	ENST00000453777.1	TSL:1	c.338C>T	p.Pro113Leu	missense	Exon 4 of 8	ENSP00000413715.1	O75019-2
	LILRA1	ENST00000473156.5	TSL:1	n.504C>T		non_coding_transcript_exon	Exon 3 of 9

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 82

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.093
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	16
DANN	Benign	0.97
DEOGEN2	Benign	0.0070	T
Eigen	Benign	-0.38
Eigen_PC	Benign	-0.67
FATHMM_MKL	Benign	0.057	N
M_CAP	Benign	0.0018	T
MetaRNN	Uncertain	0.45	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Pathogenic	3.2	M
PhyloP100		0.77
PrimateAI	Benign	0.34	T
PROVEAN	Pathogenic	-8.3	D
REVEL	Benign	0.13
Sift	Uncertain	0.020	D
Sift4G	Uncertain	0.016	D
Polyphen		0.99	D
Vest4		0.21
MutPred		0.52		Loss of disorder (P = 0.0384)
MVP		0.46
MPC		0.13
ClinPred		0.90	D
GERP RS		0.51
Varity_R		0.17
gMVP		0.053
Mutation Taster		=98/2	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

hg19: chr19-55106397;