19-54276833-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.1454G>A(p.Arg485Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,613,754 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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152000Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000522 AC: 13AN: 248880Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134706
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461754Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727172
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152000Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74232
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1457G>A (p.R486Q) 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 1457, causing the arginine (R) at amino acid position 486 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