dbSNP rs9622682: LGALS1:c.90-56G>A (chr22-37678427-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002305.4(LGALS1):c.90-56G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 1,582,550 control chromosomes in the GnomAD database, including 156,039 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 0.48 ( 18374 hom., cov: 32)

Exomes 𝑓: 0.44 ( 137665 hom. )

Consequence

LGALS1
NM_002305.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.85

Publications

16 publications found

Variant links:

Genes affected

LGALS1 (HGNC:6561): (galectin 1) The galectins are a family of beta-galactoside-binding proteins implicated in modulating cell-cell and cell-matrix interactions. This gene product may act as an autocrine negative growth factor that regulates cell proliferation. [provided by RefSeq, Jul 2008]

LGALS1 links:

Genome browser will be placed here

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002305.4. 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
	LGALS1	NM_002305.4	MANE Select	c.90-56G>A		intron	N/A	NP_002296.1	P09382

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LGALS1	ENST00000215909.10	TSL:1 MANE Select	c.90-56G>A	intron	N/A	ENSP00000215909.5	P09382
LGALS1	ENST00000895126.1		c.96-56G>A	intron	N/A	ENSP00000565185.1
LGALS1	ENST00000895125.1		c.90-56G>A	intron	N/A	ENSP00000565184.1

Frequencies

GnomAD3 genomes

AF:

0.484

AC:

73492

AN:

151962

Hom.:

18363

Cov.:

show subpopulations

Gnomad AFR

AF:

0.622

Gnomad AMI

AF:

0.503

Gnomad AMR

AF:

0.444

Gnomad ASJ

AF:

0.517

Gnomad EAS

AF:

0.492

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.383

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.425

Gnomad OTH

AF:

0.481

GnomAD2 exomes

AF:

0.447

AC:

106582

AN:

238308

AF XY:

0.444

show subpopulations

Gnomad AFR exome

AF:

0.628

Gnomad AMR exome

AF:

0.433

Gnomad ASJ exome

AF:

0.515

Gnomad EAS exome

AF:

0.512

Gnomad FIN exome

AF:

0.384

Gnomad NFE exome

AF:

0.426

Gnomad OTH exome

AF:

0.444

GnomAD4 exome

AF:

0.437

AC:

625004

AN:

1430470

Hom.:

137665

Cov.:

AF XY:

0.436

AC XY:

310469

AN XY:

712710

show subpopulations

African (AFR)

AF:

0.633

AC:

20750

AN:

32762

American (AMR)

AF:

0.436

AC:

19134

AN:

43878

Ashkenazi Jewish (ASJ)

AF:

0.512

AC:

13235

AN:

25864

East Asian (EAS)

AF:

0.518

AC:

20283

AN:

39140

South Asian (SAS)

AF:

0.427

AC:

36307

AN:

85000

European-Finnish (FIN)

AF:

0.386

AC:

20098

AN:

52082

Middle Eastern (MID)

AF:

0.439

AC:

2511

AN:

5724

European-Non Finnish (NFE)

AF:

0.429

AC:

465878

AN:

1086678

Other (OTH)

AF:

0.452

AC:

26808

AN:

59342

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

18824

37647

56471

75294

94118

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14280

28560

42840

57120

71400

<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:

0.484

AC:

73542

AN:

152080

Hom.:

18374

Cov.:

AF XY:

0.480

AC XY:

35678

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.622

AC:

25816

AN:

41492

American (AMR)

AF:

0.443

AC:

6778

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.517

AC:

1795

AN:

3470

East Asian (EAS)

AF:

0.492

AC:

2537

AN:

5160

South Asian (SAS)

AF:

0.426

AC:

2055

AN:

4826

European-Finnish (FIN)

AF:

0.383

AC:

4046

AN:

10564

Middle Eastern (MID)

AF:

0.469

AC:

138

AN:

294

European-Non Finnish (NFE)

AF:

0.425

AC:

28908

AN:

67966

Other (OTH)

AF:

0.479

AC:

1012

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1907

3814

5722

7629

9536

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

658

1316

1974

2632

3290

<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:

0.454

Hom.:

6981

Bravo

AF:

0.495

Asia WGS

AF:

0.477

AC:

1663

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.47

(source)

DANN

Benign

0.66

PhyloP100

-1.9

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