19-39658464-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001190441.3(LGALS16):c.97G>A(p.Glu33Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000363 in 1,596,260 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LGALS16 | NM_001190441.3 | c.97G>A | p.Glu33Lys | missense_variant | 3/4 | ENST00000392051.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGALS16 | ENST00000392051.4 | c.97G>A | p.Glu33Lys | missense_variant | 3/4 | 1 | NM_001190441.3 | P1 | |
LGALS16 | ENST00000594480.1 | c.152G>A | p.Arg51Gln | missense_variant, NMD_transcript_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000744 AC: 17AN: 228348Hom.: 0 AF XY: 0.0000972 AC XY: 12AN XY: 123414
GnomAD4 exome AF: 0.0000180 AC: 26AN: 1444022Hom.: 0 Cov.: 32 AF XY: 0.0000223 AC XY: 16AN XY: 717484
GnomAD4 genome AF: 0.000210 AC: 32AN: 152238Hom.: 1 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2023 | The c.97G>A (p.E33K) alteration is located in exon 3 (coding exon 3) of the LGALS16 gene. This alteration results from a G to A substitution at nucleotide position 97, causing the glutamic acid (E) at amino acid position 33 to be replaced by a lysine (K). 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