chr19-54276839-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001080978.4(LILRB2):c.1448G>A(p.Arg483Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000088 in 1,613,898 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080978.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LILRB2 | NM_001080978.4 | c.1448G>A | p.Arg483Gln | missense_variant | 10/14 | ENST00000314446.10 | NP_001074447.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LILRB2 | ENST00000314446.10 | c.1448G>A | p.Arg483Gln | missense_variant | 10/14 | 1 | NM_001080978.4 | ENSP00000319960 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152008Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000177 AC: 44AN: 248908Hom.: 0 AF XY: 0.000252 AC XY: 34AN XY: 134738
GnomAD4 exome AF: 0.0000903 AC: 132AN: 1461772Hom.: 2 Cov.: 31 AF XY: 0.000129 AC XY: 94AN XY: 727194
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152126Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 8AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 10, 2024 | The c.1451G>A (p.R484Q) alteration is located in exon 10 (coding exon 9) of the LILRB2 gene. This alteration results from a G to A substitution at nucleotide position 1451, causing the arginine (R) at amino acid position 484 to be replaced by a glutamine (Q). 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