17-20451525-T-A
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001367292.2(LGALS9B):c.880A>T(p.Ser294Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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
Genomes: not found (cov: 13)
Exomes 𝑓: 0.000017 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LGALS9B
NM_001367292.2 missense
NM_001367292.2 missense
Scores
1
16
Clinical Significance
Conservation
PhyloP100: 0.184
Genes affected
LGALS9B (HGNC:24842): (galectin 9B) This gene was initially thought to represent a pseudogene of galectin 9; however, this transcript has good exon-intron structure and encodes a predicted protein of the same size as and highly similar to galectin 9. This gene is one of two similar loci on chromosome 17p similar to galectin 9 and now thought to be protein-encoding. This gene is the more centromeric gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.22627479).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LGALS9B | NM_001367292.2 | c.880A>T | p.Ser294Cys | missense_variant | 10/11 | ENST00000423676.8 | NP_001354221.1 | |
LGALS9B | NM_001042685.3 | c.877A>T | p.Ser293Cys | missense_variant | 10/11 | NP_001036150.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LGALS9B | ENST00000423676.8 | c.880A>T | p.Ser294Cys | missense_variant | 10/11 | 1 | NM_001367292.2 | ENSP00000388841.3 | ||
LGALS9B | ENST00000324290.5 | c.877A>T | p.Ser293Cys | missense_variant | 10/11 | 5 | ENSP00000315564.5 | |||
LGALS9B | ENST00000578481.5 | n.*680A>T | non_coding_transcript_exon_variant | 9/10 | 2 | ENSP00000464627.1 | ||||
LGALS9B | ENST00000578481.5 | n.*680A>T | 3_prime_UTR_variant | 9/10 | 2 | ENSP00000464627.1 |
Frequencies
GnomAD3 genomes Cov.: 13
GnomAD3 genomes
Cov.:
13
GnomAD3 exomes AF: 0.00000418 AC: 1AN: 239428Hom.: 0 AF XY: 0.00000766 AC XY: 1AN XY: 130618
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000171 AC: 25AN: 1458224Hom.: 0 Cov.: 35 AF XY: 0.0000179 AC XY: 13AN XY: 725204
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome Cov.: 13
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Cov.:
13
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.877A>T (p.S293C) alteration is located in exon 10 (coding exon 10) of the LGALS9B gene. This alteration results from a A to T substitution at nucleotide position 877, causing the serine (S) at amino acid position 293 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
PrimateAI
Benign
T
REVEL
Benign
Sift4G
Benign
T;T
Polyphen
D;D
Vest4
MutPred
Loss of disorder (P = 8e-04);.;
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at