rs779017810

Variant names:

• chr17-18488984-C-A
• rs779017810
• NM_001040078.3:c.488C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-18488984-C-A
• chr17-18488984-C-G
• chr17-18488984-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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. 16/22 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040078.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LGALS9C	NM_001040078.3	MANE Select	c.488C>A	p.Pro163Gln	missense	Exon 5 of 11	NP_001035167.2	Q6DKI2
	LGALS9C	NM_001438918.1		c.488C>A	p.Pro163Gln	missense	Exon 5 of 11	NP_001425847.1
	LGALS9C	NM_001438921.1		c.488C>A	p.Pro163Gln	missense	Exon 5 of 11	NP_001425850.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LGALS9C	ENST00000328114.11	TSL:1 MANE Select	c.488C>A	p.Pro163Gln	missense	Exon 5 of 11	ENSP00000329932.6	Q6DKI2
	LGALS9C	ENST00000892832.1		c.488C>A	p.Pro163Gln	missense	Exon 5 of 11	ENSP00000562891.1
	LGALS9C	ENST00000583322.5	TSL:5	c.444+1227C>A		intron	N/A	ENSP00000462708.1	J3KSY2

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

African (AFR) AF: 0.00 AC: 0 AN: 32822

American (AMR) AF: 0.00 AC: 0 AN: 43494

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24304

East Asian (EAS) AF: 0.00 AC: 0 AN: 39626

South Asian (SAS) AF: 0.00 AC: 0 AN: 82056

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49394

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3950

European-Non Finnish (NFE) AF: 9.68e-7 AC: 1 AN: 1032820

Other (OTH) AF: 0.00 AC: 0 AN: 56754

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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
PhyloP100		0.41
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

Other links and lift over

dbSNP: rs779017810; hg19: chr17-18392298;