chr15-74821138-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021819.3(LMAN1L):c.971G>A(p.Arg324Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000016 in 1,559,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R324W) has been classified as Uncertain significance.
Frequency
Consequence
NM_021819.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMAN1L | NM_021819.3 | c.971G>A | p.Arg324Gln | missense_variant | 9/14 | ENST00000309664.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMAN1L | ENST00000309664.10 | c.971G>A | p.Arg324Gln | missense_variant | 9/14 | 1 | NM_021819.3 | P1 | |
LMAN1L | ENST00000379709.7 | c.935G>A | p.Arg312Gln | missense_variant | 8/13 | 1 | |||
LMAN1L | ENST00000567848.1 | c.14G>A | p.Arg5Gln | missense_variant | 1/4 | 4 | |||
LMAN1L | ENST00000565585.5 | n.1365G>A | non_coding_transcript_exon_variant | 2/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000180 AC: 3AN: 166358Hom.: 0 AF XY: 0.0000113 AC XY: 1AN XY: 88148
GnomAD4 exome AF: 0.0000156 AC: 22AN: 1407674Hom.: 0 Cov.: 31 AF XY: 0.0000187 AC XY: 13AN XY: 695198
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74334
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 02, 2023 | 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