19-54636494-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001081637.3(LILRB1):c.1654C>A(p.Gln552Lys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000627 in 1,611,288 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001081637.3 missense, splice_region
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LILRB1 | NM_001081637.3 | c.1654C>A | p.Gln552Lys | missense_variant, splice_region_variant | Exon 14 of 15 | ENST00000324602.12 | NP_001075106.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LILRB1 | ENST00000324602.12 | c.1654C>A | p.Gln552Lys | missense_variant, splice_region_variant | Exon 14 of 15 | 5 | NM_001081637.3 | ENSP00000315997.7 |
Frequencies
GnomAD3 genomes AF: 0.000231 AC: 35AN: 151820Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000727 AC: 18AN: 247628Hom.: 0 AF XY: 0.0000598 AC XY: 8AN XY: 133728
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1459468Hom.: 1 Cov.: 39 AF XY: 0.0000344 AC XY: 25AN XY: 726040
GnomAD4 genome AF: 0.000231 AC: 35AN: 151820Hom.: 0 Cov.: 31 AF XY: 0.000256 AC XY: 19AN XY: 74146
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1654C>A (p.Q552K) alteration is located in exon 14 (coding exon 13) of the LILRB1 gene. This alteration results from a C to A substitution at nucleotide position 1654, causing the glutamine (Q) at amino acid position 552 to be replaced by a lysine (K). 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