dbSNP rs4794976: LGALS9:c.921+87T>G (chr17-27647519-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_009587.3(LGALS9):c.921+87T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 1,545,042 control chromosomes in the GnomAD database, including 90,819 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 8400 hom., cov: 31)

Exomes 𝑓: 0.34 ( 82419 hom. )

Consequence

LGALS9
NM_009587.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.188

Publications

11 publications found

Variant links:

Genes affected

LGALS9 (HGNC:6570): (galectin 9) The galectins are a family of beta-galactoside-binding proteins implicated in modulating cell-cell and cell-matrix interactions. The protein encoded by this gene is an S-type lectin. It is overexpressed in Hodgkin's disease tissue and might participate in the interaction between the H&RS cells with their surrounding cells and might thus play a role in the pathogenesis of this disease and/or its associated immunodeficiency. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]

LGALS9 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_009587.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LGALS9	NM_009587.3	MANE Select	c.921+87T>G	intron	N/A	NP_033665.1
LGALS9	NM_002308.4		c.825+87T>G	intron	N/A	NP_002299.2
LGALS9	NM_001330163.2		c.662+401T>G	intron	N/A	NP_001317092.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LGALS9	ENST00000395473.7	TSL:1 MANE Select	c.921+87T>G	intron	N/A	ENSP00000378856.2
LGALS9	ENST00000302228.9	TSL:1	c.825+87T>G	intron	N/A	ENSP00000306228.5
LGALS9	ENST00000481514.5	TSL:1	n.1630+87T>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.326

AC:

49530

AN:

151710

Hom.:

8373

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.201

Gnomad AMR

AF:

0.388

Gnomad ASJ

AF:

0.369

Gnomad EAS

AF:

0.486

Gnomad SAS

AF:

0.566

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.311

Gnomad OTH

AF:

0.343

GnomAD4 exome

AF:

0.337

AC:

469559

AN:

1393214

Hom.:

82419

AF XY:

0.343

AC XY:

236356

AN XY:

688340

show subpopulations

African (AFR)

AF:

0.287

AC:

9030

AN:

31472

American (AMR)

AF:

0.410

AC:

14783

AN:

36016

Ashkenazi Jewish (ASJ)

AF:

0.379

AC:

9265

AN:

24444

East Asian (EAS)

AF:

0.548

AC:

20160

AN:

36770

South Asian (SAS)

AF:

0.557

AC:

44399

AN:

79706

European-Finnish (FIN)

AF:

0.305

AC:

15272

AN:

50106

Middle Eastern (MID)

AF:

0.341

AC:

1909

AN:

5596

European-Non Finnish (NFE)

AF:

0.312

AC:

334497

AN:

1071336

Other (OTH)

AF:

0.350

AC:

20244

AN:

57768

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

15063

30126

45190

60253

75316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11282

22564

33846

45128

56410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.327

AC:

49608

AN:

151828

Hom.:

8400

Cov.:

AF XY:

0.332

AC XY:

24615

AN XY:

74194

show subpopulations

African (AFR)

AF:

0.283

AC:

11737

AN:

41402

American (AMR)

AF:

0.389

AC:

5935

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.369

AC:

1281

AN:

3468

East Asian (EAS)

AF:

0.486

AC:

2495

AN:

5138

South Asian (SAS)

AF:

0.567

AC:

2727

AN:

4812

European-Finnish (FIN)

AF:

0.315

AC:

3314

AN:

10534

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.311

AC:

21116

AN:

67918

Other (OTH)

AF:

0.350

AC:

736

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1690

3379

5069

6758

8448

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.331

Hom.:

4790

Bravo

AF:

0.325

Asia WGS

AF:

0.550

AC:

1911

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.9

(source)

DANN

Benign

0.67

PhyloP100

-0.19

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over