19-54252957-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001081442.3(LILRB5):c.1388G>A(p.Gly463Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000701 in 1,569,718 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001081442.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LILRB5 | NM_001081442.3 | c.1388G>A | p.Gly463Glu | missense_variant | Exon 9 of 13 | ENST00000449561.3 | NP_001074911.2 | |
LILRB5 | NM_001304457.3 | c.1361G>A | p.Gly454Glu | missense_variant | Exon 9 of 13 | NP_001291386.2 | ||
LILRB5 | NM_006840.5 | c.1385G>A | p.Gly462Glu | missense_variant | Exon 9 of 13 | NP_006831.2 | ||
LILRB5 | NM_001081443.3 | c.1088G>A | p.Gly363Glu | missense_variant | Exon 8 of 12 | NP_001074912.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248546Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134592
GnomAD4 exome AF: 0.00000353 AC: 5AN: 1417616Hom.: 0 Cov.: 30 AF XY: 0.00000142 AC XY: 1AN XY: 705364
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1388G>A (p.G463E) alteration is located in exon 9 (coding exon 9) of the LILRB5 gene. This alteration results from a G to A substitution at nucleotide position 1388, causing the glycine (G) at amino acid position 463 to be replaced by a glutamic acid (E). 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