Variant 17-18487709-CA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The ENST00000328114.11(LGALS9C):c.397del(p.Thr133ProfsTer85) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000733 in 140,604 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.00073 ( 3 hom., cov: 21)

Exomes 𝑓: 0.0013 ( 102 hom. )

Failed GnomAD Quality Control

Consequence

LGALS9C
ENST00000328114.11 frameshift

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.27

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]

LGALS9C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 17-18487709-CA-C is Benign according to our data. Variant chr17-18487709-CA-C is described in ClinVar as [Likely_benign]. Clinvar id is 2647558.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LGALS9C	NM_001040078.3 linkuse as main transcript	c.397del	p.Thr133ProfsTer85	frameshift_variant	4/11	ENST00000328114.11	NP_001035167.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LGALS9C	ENST00000328114.11 linkuse as main transcript	c.397del	p.Thr133ProfsTer85	frameshift_variant	4/11	1	NM_001040078.3	ENSP00000329932	P2

Frequencies

GnomAD3 genomes

AF:

0.000733

AC:

103

AN:

140520

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000221

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000142

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000211

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00145

Gnomad OTH

AF:

0.00104

GnomAD3 exomes

AF:

0.000702

AC:

162

AN:

230628

Hom.:

AF XY:

0.000601

AC XY:

AN XY:

124824

show subpopulations

Gnomad AFR exome

AF:

0.000126

Gnomad AMR exome

AF:

0.000367

Gnomad ASJ exome

AF:

0.000108

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000447

Gnomad NFE exome

AF:

0.00134

Gnomad OTH exome

AF:

0.000535

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00135

AC:

1907

AN:

1416838

Hom.:

102

Cov.:

AF XY:

0.00128

AC XY:

901

AN XY:

704438

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000624

Gnomad4 ASJ exome

AF:

0.000119

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000119

Gnomad4 FIN exome

AF:

0.000502

Gnomad4 NFE exome

AF:

0.00163

Gnomad4 OTH exome

AF:

0.00167

GnomAD4 genome

AF:

0.000733

AC:

103

AN:

140604

Hom.:

Cov.:

AF XY:

0.000672

AC XY:

AN XY:

68446

show subpopulations

Gnomad4 AFR

AF:

0.000221

Gnomad4 AMR

AF:

0.000142

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000211

Gnomad4 NFE

AF:

0.00145

Gnomad4 OTH

AF:

0.00104

Alfa

AF:

0.000518

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

LGALS9C: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over