5-135947437-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_002302.3(LECT2):c.350G>T(p.Gly117Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000041 in 1,461,760 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002302.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251398Hom.: 1 AF XY: 0.0000294 AC XY: 4AN XY: 135874
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461760Hom.: 1 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727178
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.350G>T (p.G117V) alteration is located in exon 4 (coding exon 4) of the LECT2 gene. This alteration results from a G to T substitution at nucleotide position 350, causing the glycine (G) at amino acid position 117 to be replaced by a valine (V). 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