19-54239031-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000396365.7(LILRA6):āc.1368G>Cā(p.Leu456Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000664 in 150,686 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000396365.7 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 |
---|---|---|---|---|---|---|---|
LILRA6 | NM_024318.5 | c.1368G>C | p.Leu456Phe | missense_variant | 8/8 | ENST00000396365.7 | |
LILRA6 | NR_104098.2 | n.1321G>C | non_coding_transcript_exon_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LILRA6 | ENST00000396365.7 | c.1368G>C | p.Leu456Phe | missense_variant | 8/8 | 1 | NM_024318.5 | P1 | |
LILRA6 | ENST00000430421.5 | c.*700G>C | 3_prime_UTR_variant, NMD_transcript_variant | 8/10 | 1 | ||||
LILRA6 | ENST00000245621.6 | c.1317G>C | p.Leu439Phe | missense_variant | 7/7 | 5 | |||
RPS9 | ENST00000448962.5 | c.*182+7095C>G | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000664 AC: 1AN: 150686Hom.: 0 Cov.: 34
GnomAD4 exome Cov.: 32
GnomAD4 genome AF: 0.00000664 AC: 1AN: 150686Hom.: 0 Cov.: 34 AF XY: 0.0000136 AC XY: 1AN XY: 73668
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.1368G>C (p.L456F) alteration is located in exon 8 (coding exon 8) of the LILRA6 gene. This alteration results from a G to C substitution at nucleotide position 1368, causing the leucine (L) at amino acid position 456 to be replaced by a phenylalanine (F). 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