19-54632106-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001081637.3(LILRB1):c.530C>T(p.Ser177Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,614,128 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_001081637.3 missense
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.530C>T | p.Ser177Leu | missense_variant | Exon 5 of 15 | ENST00000324602.12 | NP_001075106.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LILRB1 | ENST00000324602.12 | c.530C>T | p.Ser177Leu | missense_variant | Exon 5 of 15 | 5 | NM_001081637.3 | ENSP00000315997.7 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152254Hom.: 0 Cov.: 41
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251482Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135916
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461874Hom.: 0 Cov.: 163 AF XY: 0.0000344 AC XY: 25AN XY: 727242
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152254Hom.: 0 Cov.: 41 AF XY: 0.0000134 AC XY: 1AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.530C>T (p.S177L) alteration is located in exon 5 (coding exon 4) of the LILRB1 gene. This alteration results from a C to T substitution at nucleotide position 530, causing the serine (S) at amino acid position 177 to be replaced by a leucine (L). 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