16-25132411-C-T
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_016309.3(LCMT1):c.215C>T(p.Ala72Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000109 in 1,461,462 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016309.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LCMT1 | ENST00000399069.8 | c.215C>T | p.Ala72Val | missense_variant | Exon 3 of 11 | 1 | NM_016309.3 | ENSP00000382021.3 | ||
LCMT1 | ENST00000380962.9 | n.*72C>T | non_coding_transcript_exon_variant | Exon 4 of 12 | 2 | ENSP00000370349.5 | ||||
LCMT1 | ENST00000380962.9 | n.*72C>T | 3_prime_UTR_variant | Exon 4 of 12 | 2 | ENSP00000370349.5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD2 exomes AF: 0.00000803 AC: 2AN: 249020 AF XY: 0.0000148 show subpopulations
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461462Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727020 show subpopulations
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.215C>T (p.A72V) alteration is located in exon 3 (coding exon 3) of the LCMT1 gene. This alteration results from a C to T substitution at nucleotide position 215, causing the alanine (A) at amino acid position 72 to be replaced by a valine (V). 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