19-54573906-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001130917.3(LILRA2):āc.28T>Cā(p.Cys10Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001130917.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LILRA2 | NM_001130917.3 | c.28T>C | p.Cys10Arg | missense_variant | 1/8 | ENST00000391738.8 | NP_001124389.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LILRA2 | ENST00000391738.8 | c.28T>C | p.Cys10Arg | missense_variant | 1/8 | 1 | NM_001130917.3 | ENSP00000375618 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152236Hom.: 0 Cov.: 41
GnomAD3 exomes AF: 0.0000757 AC: 19AN: 250980Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135654
GnomAD4 exome AF: 0.000120 AC: 175AN: 1461820Hom.: 0 Cov.: 158 AF XY: 0.000100 AC XY: 73AN XY: 727212
GnomAD4 genome AF: 0.000151 AC: 23AN: 152236Hom.: 0 Cov.: 41 AF XY: 0.000148 AC XY: 11AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2022 | The c.28T>C (p.C10R) alteration is located in exon 1 (coding exon 1) of the LILRA2 gene. This alteration results from a T to C substitution at nucleotide position 28, causing the cysteine (C) at amino acid position 10 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at