chr19-54276830-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080978.4(LILRB2):c.1457G>A(p.Arg486His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LILRB2 | NM_001080978.4 | c.1457G>A | p.Arg486His | 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.1457G>A | p.Arg486His | missense_variant | 10/14 | 1 | NM_001080978.4 | ENSP00000319960 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152018Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248832Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134680
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461730Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727162
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152018Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2023 | The c.1460G>A (p.R487H) 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 1460, causing the arginine (R) at amino acid position 487 to be replaced by a histidine (H). 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