rs779017810

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001040078.3(LGALS9C):​c.488C>A​(p.Pro163Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000732 in 1,365,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. P163L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 22)
Exomes 𝑓: 7.3e-7 ( 0 hom. )

Consequence

LGALS9C
NM_001040078.3 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.409
Variant links:
Genes affected
LGALS9C (HGNC:33874): (galectin 9C) 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 telomeric gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.057917893).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LGALS9CNM_001040078.3 linkc.488C>A p.Pro163Gln missense_variant Exon 5 of 11 ENST00000328114.11 NP_001035167.2 Q6DKI2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LGALS9CENST00000328114.11 linkc.488C>A p.Pro163Gln missense_variant Exon 5 of 11 1 NM_001040078.3 ENSP00000329932.6 Q6DKI2

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD4 exome
AF:
7.32e-7
AC:
1
AN:
1365220
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
679344
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.68e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.094
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.71
CADD
Benign
0.59
DANN
Benign
0.098
DEOGEN2
Benign
0.0094
T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.00064
N
M_CAP
Benign
0.0028
T
MetaRNN
Benign
0.058
T
MetaSVM
Benign
-0.91
T
MutationAssessor
Benign
-0.34
N
PrimateAI
Benign
0.24
T
PROVEAN
Benign
0.18
N
REVEL
Benign
0.011
Sift
Benign
0.64
T
Sift4G
Benign
0.29
T
Polyphen
0.0060
B
Vest4
0.23
MutPred
0.18
Loss of glycosylation at S160 (P = 0.0674);
MVP
0.043
ClinPred
0.026
T
GERP RS
0.38
Varity_R
0.028
gMVP
0.13

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-18392298; API