19-39657925-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001190441.3(LGALS16):c.58G>A(p.Val20Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001190441.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LGALS16 | NM_001190441.3 | c.58G>A | p.Val20Met | missense_variant | 2/4 | ENST00000392051.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGALS16 | ENST00000392051.4 | c.58G>A | p.Val20Met | missense_variant | 2/4 | 1 | NM_001190441.3 | P1 | |
LGALS16 | ENST00000594480.1 | c.113G>A | p.Arg38His | missense_variant, NMD_transcript_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251272Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135800
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1461660Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 727134
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.58G>A (p.V20M) alteration is located in exon 2 (coding exon 2) of the LGALS16 gene. This alteration results from a G to A substitution at nucleotide position 58, causing the valine (V) at amino acid position 20 to be replaced by a methionine (M). 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