16-25169163-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_016309.3(LCMT1):c.742C>A(p.Arg248Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,238 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R248C) has been classified as Uncertain significance.
Frequency
Consequence
NM_016309.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCMT1 | NM_016309.3 | c.742C>A | p.Arg248Ser | missense_variant | 8/11 | ENST00000399069.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCMT1 | ENST00000399069.8 | c.742C>A | p.Arg248Ser | missense_variant | 8/11 | 1 | NM_016309.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249156Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135164
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461238Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726906
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 13, 2023 | The c.742C>A (p.R248S) alteration is located in exon 8 (coding exon 8) of the LCMT1 gene. This alteration results from a C to A substitution at nucleotide position 742, causing the arginine (R) at amino acid position 248 to be replaced by a serine (S). 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