17-18488984-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001040078.3(LGALS9C):c.488C>T(p.Pro163Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 Uncertain significance (★).
Frequency
Consequence
NM_001040078.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000725 AC: 1AN: 137922Hom.: 0 Cov.: 22
GnomAD3 exomes AF: 0.000144 AC: 34AN: 236930Hom.: 5 AF XY: 0.000109 AC XY: 14AN XY: 128066
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000498 AC: 68AN: 1365214Hom.: 7 Cov.: 32 AF XY: 0.0000397 AC XY: 27AN XY: 679342
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000724 AC: 1AN: 138042Hom.: 0 Cov.: 22 AF XY: 0.0000149 AC XY: 1AN XY: 67218
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.488C>T (p.P163L) alteration is located in exon 5 (coding exon 5) of the LGALS9C gene. This alteration results from a C to T substitution at nucleotide position 488, causing the proline (P) at amino acid position 163 to be replaced by a leucine (L). 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