5-135951340-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002302.3(LECT2):c.172A>G(p.Ile58Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 1,612,554 control chromosomes in the GnomAD database, including 320,989 homozygotes. 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002302.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LECT2 | NM_002302.3 | c.172A>G | p.Ile58Val | missense_variant | 3/4 | ENST00000274507.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LECT2 | ENST00000274507.6 | c.172A>G | p.Ile58Val | missense_variant | 3/4 | 1 | NM_002302.3 | P1 | |
ENST00000467490.5 | n.1491T>C | non_coding_transcript_exon_variant | 7/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.619 AC: 94004AN: 151920Hom.: 29301 Cov.: 32
GnomAD3 exomes AF: 0.645 AC: 161816AN: 251034Hom.: 52372 AF XY: 0.645 AC XY: 87525AN XY: 135636
GnomAD4 exome AF: 0.631 AC: 921347AN: 1460516Hom.: 291665 Cov.: 39 AF XY: 0.632 AC XY: 459492AN XY: 726604
GnomAD4 genome ? AF: 0.619 AC: 94062AN: 152038Hom.: 29324 Cov.: 32 AF XY: 0.622 AC XY: 46185AN XY: 74310
ClinVar
Submissions by phenotype
LECT2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at