chr6-143857380-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032860.5(LTV1):c.475C>T(p.Leu159Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,796 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032860.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LTV1 | ENST00000367576.6 | c.475C>T | p.Leu159Phe | missense_variant | Exon 5 of 11 | 1 | NM_032860.5 | ENSP00000356548.5 | ||
ENSG00000280148 | ENST00000454207.2 | n.-54C>T | non_coding_transcript_exon_variant | Exon 1 of 10 | 2 | ENSP00000400756.2 | ||||
ENSG00000280148 | ENST00000454207.2 | n.-54C>T | 5_prime_UTR_variant | Exon 1 of 10 | 2 | ENSP00000400756.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461796Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727200
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.475C>T (p.L159F) alteration is located in exon 5 (coding exon 5) of the LTV1 gene. This alteration results from a C to T substitution at nucleotide position 475, causing the leucine (L) at amino acid position 159 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