Variant chr17-20467454-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001367292.2(LGALS9B):c.17C>G(p.Ser6Cys) 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 Benign (★).

Frequency

Genomes: 𝑓 0.80 ( 15379 hom., cov: 7)

Exomes 𝑓: 0.72 ( 120350 hom. )

Failed GnomAD Quality Control

Consequence

LGALS9B
NM_001367292.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.471

Variant links:

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]

LGALS9B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.35666E-6).

BP6

Variant 17-20467454-G-C is Benign according to our data. Variant chr17-20467454-G-C is described in ClinVar as [Benign]. Clinvar id is 403031.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LGALS9B	NM_001367292.2 linkuse as main transcript	c.17C>G	p.Ser6Cys	missense_variant	1/11	ENST00000423676.8
LGALS9B	NM_001042685.3 linkuse as main transcript	c.17C>G	p.Ser6Cys	missense_variant	1/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LGALS9B	ENST00000423676.8 linkuse as main transcript	c.17C>G	p.Ser6Cys	missense_variant	1/11	1	NM_001367292.2	P4	Q3B8N2-1
LGALS9B	ENST00000324290.5 linkuse as main transcript	c.17C>G	p.Ser6Cys	missense_variant	1/11	5		A1	Q3B8N2-2
LGALS9B	ENST00000578481.5 linkuse as main transcript	c.17C>G	p.Ser6Cys	missense_variant, NMD_transcript_variant	1/10	2

Frequencies

GnomAD3 genomes

AF:

0.797

AC:

36983

AN:

46382

Hom.:

15372

Cov.:

show subpopulations

Gnomad AFR

AF:

0.673

Gnomad AMI

AF:

0.836

Gnomad AMR

AF:

0.728

Gnomad ASJ

AF:

0.862

Gnomad EAS

AF:

0.394

Gnomad SAS

AF:

0.859

Gnomad FIN

AF:

0.882

Gnomad MID

AF:

0.877

Gnomad NFE

AF:

0.862

Gnomad OTH

AF:

0.805

GnomAD3 exomes

AF:

0.834

AC:

50177

AN:

60144

Hom.:

22977

AF XY:

0.838

AC XY:

25309

AN XY:

30200

show subpopulations

Gnomad AFR exome

AF:

0.815

Gnomad AMR exome

AF:

0.745

Gnomad ASJ exome

AF:

0.923

Gnomad EAS exome

AF:

0.341

Gnomad SAS exome

AF:

0.923

Gnomad FIN exome

AF:

0.936

Gnomad NFE exome

AF:

0.931

Gnomad OTH exome

AF:

0.882

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.724

AC:

279969

AN:

386744

Hom.:

120350

Cov.:

AF XY:

0.733

AC XY:

143814

AN XY:

196282

show subpopulations

Gnomad4 AFR exome

AF:

0.521

Gnomad4 AMR exome

AF:

0.596

Gnomad4 ASJ exome

AF:

0.792

Gnomad4 EAS exome

AF:

0.332

Gnomad4 SAS exome

AF:

0.822

Gnomad4 FIN exome

AF:

0.909

Gnomad4 NFE exome

AF:

0.730

Gnomad4 OTH exome

AF:

0.746

GnomAD4 genome

AF:

0.797

AC:

36997

AN:

46404

Hom.:

15379

Cov.:

AF XY:

0.787

AC XY:

16896

AN XY:

21462

show subpopulations

Gnomad4 AFR

AF:

0.673

Gnomad4 AMR

AF:

0.728

Gnomad4 ASJ

AF:

0.862

Gnomad4 EAS

AF:

0.392

Gnomad4 SAS

AF:

0.859

Gnomad4 FIN

AF:

0.882

Gnomad4 NFE

AF:

0.862

Gnomad4 OTH

AF:

0.804

ExAC

AF:

0.772

AC:

37863

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.060

BayesDel_addAF

Benign

-0.34

BayesDel_noAF

Benign

-0.73

CADD

Benign

3.3

DANN

Benign

0.73

DEOGEN2

Benign

0.0057

T;.

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.0067

LIST_S2

Benign

0.18

T;T

MetaRNN

Benign

0.0000014

T;T

MetaSVM

Benign

-0.94

MutationAssessor

Uncertain

2.1

M;M

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.46

PROVEAN

Benign

-1.4

N;N

REVEL

Benign

0.015

Sift

Benign

0.086

T;T

Sift4G

Benign

0.17

T;T

Polyphen

0.0

B;B

Vest4

0.062

ClinPred

0.0073

GERP RS

-0.15

Varity_R

0.066

gMVP

0.15

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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