rs31517
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002302.3(LECT2):āc.172A>Gā(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 (ā ). 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
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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