6-143857832-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032860.5(LTV1):c.620C>A(p.Ala207Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LTV1 | ENST00000367576.6 | c.620C>A | p.Ala207Glu | missense_variant | Exon 6 of 11 | 1 | NM_032860.5 | ENSP00000356548.5 | ||
ENSG00000280148 | ENST00000454207.2 | n.92C>A | non_coding_transcript_exon_variant | Exon 2 of 10 | 2 | ENSP00000400756.2 | ||||
ENSG00000270890 | ENST00000604280.1 | n.*230G>T | downstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461778Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727206
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.620C>A (p.A207E) alteration is located in exon 6 (coding exon 6) of the LTV1 gene. This alteration results from a C to A substitution at nucleotide position 620, causing the alanine (A) at amino acid position 207 to be replaced by a glutamic acid (E). 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