19-54336982-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_012276.5(LILRA4):c.1114G>A(p.Gly372Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000968 in 1,457,326 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_012276.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LILRA4 | ENST00000291759.5 | c.1114G>A | p.Gly372Arg | missense_variant | Exon 6 of 8 | 2 | NM_012276.5 | ENSP00000291759.4 | ||
LILRA4 | ENST00000595581.1 | n.211G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 | ENSP00000471722.1 | ||||
ENSG00000275210 | ENST00000616950.1 | n.187G>A | non_coding_transcript_exon_variant | Exon 1 of 8 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000239 AC: 33AN: 138288Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000151 AC: 38AN: 251462Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135902
GnomAD4 exome AF: 0.0000789 AC: 104AN: 1318924Hom.: 0 Cov.: 103 AF XY: 0.000101 AC XY: 67AN XY: 660142
GnomAD4 genome AF: 0.000267 AC: 37AN: 138402Hom.: 0 Cov.: 32 AF XY: 0.000326 AC XY: 22AN XY: 67386
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at