Genetic Variant LGALS9:c.759-38T>C (chr17-27647232-T-C) – 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.759-38T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 1,612,944 control chromosomes in the GnomAD database, including 106,023 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 ( 8509 hom., cov: 32)

Exomes 𝑓: 0.36 ( 97514 hom. )

Consequence

LGALS9
NM_009587.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0200

Publications

23 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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LGALS9	NM_009587.3 link	c.759-38T>C		intron_variant	Intron 9 of 10	ENST00000395473.7	NP_033665.1	O00182-1A0A024QZ55

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LGALS9	ENST00000395473.7 link	c.759-38T>C		intron_variant	Intron 9 of 10	1	NM_009587.3	ENSP00000378856.2		O00182-1

Frequencies

GnomAD3 genomes

AF:

0.329

AC:

50030

AN:

151884

Hom.:

8502

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.341

Gnomad AMR

AF:

0.406

Gnomad ASJ

AF:

0.396

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.366

Gnomad OTH

AF:

0.365

GnomAD2 exomes

AF:

0.359

AC:

90095

AN:

250744

AF XY:

0.361

show subpopulations

Gnomad AFR exome

AF:

0.227

Gnomad AMR exome

AF:

0.427

Gnomad ASJ exome

AF:

0.406

Gnomad EAS exome

AF:

0.298

Gnomad FIN exome

AF:

0.328

Gnomad NFE exome

AF:

0.366

Gnomad OTH exome

AF:

0.370

GnomAD4 exome

AF:

0.363

AC:

530765

AN:

1460942

Hom.:

97514

Cov.:

AF XY:

0.363

AC XY:

264104

AN XY:

726776

show subpopulations

African (AFR)

AF:

0.232

AC:

7772

AN:

33462

American (AMR)

AF:

0.426

AC:

19033

AN:

44686

Ashkenazi Jewish (ASJ)

AF:

0.407

AC:

10647

AN:

26134

East Asian (EAS)

AF:

0.305

AC:

12090

AN:

39692

South Asian (SAS)

AF:

0.372

AC:

32082

AN:

86218

European-Finnish (FIN)

AF:

0.325

AC:

17372

AN:

53392

Middle Eastern (MID)

AF:

0.432

AC:

2241

AN:

5188

European-Non Finnish (NFE)

AF:

0.367

AC:

407714

AN:

1111854

Other (OTH)

AF:

0.362

AC:

21814

AN:

60316

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

23141

46283

69424

92566

115707

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12908

25816

38724

51632

64540

<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:

0.329

AC:

50057

AN:

152002

Hom.:

8509

Cov.:

AF XY:

0.327

AC XY:

24267

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.232

AC:

9624

AN:

41450

American (AMR)

AF:

0.407

AC:

6216

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.396

AC:

1374

AN:

3470

East Asian (EAS)

AF:

0.282

AC:

1450

AN:

5144

South Asian (SAS)

AF:

0.372

AC:

1791

AN:

4820

European-Finnish (FIN)

AF:

0.332

AC:

3508

AN:

10564

Middle Eastern (MID)

AF:

0.439

AC:

129

AN:

294

European-Non Finnish (NFE)

AF:

0.366

AC:

24891

AN:

67956

Other (OTH)

AF:

0.361

AC:

763

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1668

3337

5005

6674

8342

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

498

996

1494

1992

2490

<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:

0.362

Hom.:

14335

Bravo

AF:

0.332

Asia WGS

AF:

0.322

AC:

1119

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.5

(source)

DANN

Benign

0.35

PhyloP100

0.020

Mutation Taster

=95/5

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over