Genetic Variant NM_002305.4: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:

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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=-0.88).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LGALS1	NM_002305.4 link	c.90-56G>A		intron_variant	Intron 2 of 3	ENST00000215909.10	NP_002296.1	P09382A0A384MR27

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LGALS1	ENST00000215909.10 link	c.90-56G>A		intron_variant	Intron 2 of 3	1	NM_002305.4	ENSP00000215909.5		P09382

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over