19-54218362-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006864.4(LILRB3):āc.1592A>Gā(p.Gln531Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,788 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_006864.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LILRB3 | NM_006864.4 | c.1592A>G | p.Gln531Arg | missense_variant, splice_region_variant | 11/13 | ENST00000445347.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LILRB3 | ENST00000445347.2 | c.1592A>G | p.Gln531Arg | missense_variant, splice_region_variant | 11/13 | 2 | NM_006864.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 152190Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251412Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135874
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461788Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727196
GnomAD4 genome ? Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2022 | The c.1592A>G (p.Q531R) alteration is located in exon 11 (coding exon 11) of the LILRB3 gene. This alteration results from a A to G substitution at nucleotide position 1592, causing the glutamine (Q) at amino acid position 531 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