17-27631278-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_009587.3(LGALS9):c.13G>A(p.Gly5Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 1,613,782 control chromosomes in the GnomAD database, including 38,482 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_009587.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LGALS9 | NM_009587.3 | c.13G>A | p.Gly5Ser | missense_variant | 1/11 | ENST00000395473.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGALS9 | ENST00000395473.7 | c.13G>A | p.Gly5Ser | missense_variant | 1/11 | 1 | NM_009587.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.194 AC: 29465AN: 152052Hom.: 3028 Cov.: 32
GnomAD3 exomes AF: 0.225 AC: 56663AN: 251364Hom.: 6800 AF XY: 0.226 AC XY: 30669AN XY: 135860
GnomAD4 exome AF: 0.218 AC: 318600AN: 1461610Hom.: 35453 Cov.: 33 AF XY: 0.219 AC XY: 158968AN XY: 727124
GnomAD4 genome AF: 0.194 AC: 29467AN: 152172Hom.: 3029 Cov.: 32 AF XY: 0.193 AC XY: 14355AN XY: 74402
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at