NM_015613.3:c.1594G>T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015613.3(LRIT1):c.1594G>T(p.Val532Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,614,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015613.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRIT1 | ENST00000372105.4 | c.1594G>T | p.Val532Leu | missense_variant | Exon 4 of 4 | 1 | NM_015613.3 | ENSP00000361177.3 | ||
RGR | ENST00000652073.1 | c.-567-162C>A | intron_variant | Intron 1 of 7 | ENSP00000498800.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251246Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135826
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.0000330 AC XY: 24AN XY: 727246
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1594G>T (p.V532L) alteration is located in exon 4 (coding exon 4) of the LRIT1 gene. This alteration results from a G to T substitution at nucleotide position 1594, causing the valine (V) at amino acid position 532 to be replaced by a leucine (L). 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