NM_006863.4:c.17C>T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006863.4(LILRA1):c.17C>T(p.Thr6Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,611,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T6K) has been classified as Uncertain significance.
Frequency
Consequence
NM_006863.4 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: 0.0000855 AC: 13AN: 152050Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000811 AC: 2AN: 246486Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133450
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1459562Hom.: 0 Cov.: 56 AF XY: 0.00000275 AC XY: 2AN XY: 726186
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152050Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74268
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at