19-54217175-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006864.4(LILRB3):āc.1814G>Cā(p.Arg605Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,613,344 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006864.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LILRB3 | NM_006864.4 | c.1814G>C | p.Arg605Pro | missense_variant | 13/13 | ENST00000445347.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LILRB3 | ENST00000445347.2 | c.1814G>C | p.Arg605Pro | missense_variant | 13/13 | 2 | NM_006864.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000462 AC: 7AN: 151470Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251442Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135912
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461874Hom.: 0 Cov.: 32 AF XY: 0.0000633 AC XY: 46AN XY: 727238
GnomAD4 genome ? AF: 0.0000462 AC: 7AN: 151470Hom.: 0 Cov.: 31 AF XY: 0.0000541 AC XY: 4AN XY: 73922
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 20, 2023 | The c.1817G>C (p.R606P) alteration is located in exon 13 (coding exon 13) of the LILRB3 gene. This alteration results from a G to C substitution at nucleotide position 1817, causing the arginine (R) at amino acid position 606 to be replaced by a proline (P). 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