19-54632613-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001081637.3(LILRB1):c.811G>A(p.Ala271Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000234 in 1,613,104 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LILRB1 | NM_001081637.3 | c.811G>A | p.Ala271Thr | missense_variant | 6/15 | ENST00000324602.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LILRB1 | ENST00000324602.12 | c.811G>A | p.Ala271Thr | missense_variant | 6/15 | 5 | NM_001081637.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000192 AC: 29AN: 151178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251456Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135898
GnomAD4 exome AF: 0.000238 AC: 348AN: 1461812Hom.: 0 Cov.: 76 AF XY: 0.000241 AC XY: 175AN XY: 727208
GnomAD4 genome ? AF: 0.000192 AC: 29AN: 151292Hom.: 0 Cov.: 33 AF XY: 0.000230 AC XY: 17AN XY: 73942
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.811G>A (p.A271T) alteration is located in exon 6 (coding exon 5) of the LILRB1 gene. This alteration results from a G to A substitution at nucleotide position 811, causing the alanine (A) at amino acid position 271 to be replaced by a threonine (T). 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