chr19-54595351-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000251372.8(LILRA1):​c.610T>C​(p.Ser204Pro) variant causes a missense 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. 12/21 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
ENST00000251372.8 missense

Scores

3
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -4.27
Variant links:
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]

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ACMG classification

Classification made for transcript

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=0.08424473).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LILRA1NM_006863.4 linkuse as main transcriptc.610T>C p.Ser204Pro missense_variant 5/10 ENST00000251372.8 NP_006854.1 O75019-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LILRA1ENST00000251372.8 linkuse as main transcriptc.610T>C p.Ser204Pro missense_variant 5/101 NM_006863.4 ENSP00000251372.3 O75019-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
87
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsSep 22, 2022The c.610T>C (p.S204P) alteration is located in exon 5 (coding exon 4) of the LILRA1 gene. This alteration results from a T to C substitution at nucleotide position 610, causing the serine (S) at amino acid position 204 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Benign
-0.30
T
BayesDel_noAF
Benign
-0.66
CADD
Benign
3.2
DANN
Uncertain
0.98
DEOGEN2
Benign
0.018
T;.
Eigen
Benign
-0.96
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.0044
N
M_CAP
Benign
0.0030
T
MetaRNN
Benign
0.084
T;T
MetaSVM
Benign
-0.96
T
MutationAssessor
Uncertain
2.4
M;M
MutationTaster
Benign
1.0
N;N;N;N;N
PrimateAI
Benign
0.33
T
PROVEAN
Uncertain
-3.3
D;D
REVEL
Benign
0.12
Sift
Benign
0.037
D;D
Sift4G
Benign
0.064
T;T
Polyphen
0.0020
B;P
Vest4
0.15
MutPred
0.49
Gain of catalytic residue at S204 (P = 0.001);Gain of catalytic residue at S204 (P = 0.001);
MVP
0.13
MPC
0.030
ClinPred
0.44
T
GERP RS
-3.2
Varity_R
0.15
gMVP
0.11

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-55106816; API