Genetic Variant NM_006149.4:c.45+48G>A (chr19-38812794-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006149.4(LGALS4):c.45+48G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,597,778 control chromosomes in the GnomAD database, including 13,401 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 0.092 ( 849 hom., cov: 32)

Exomes 𝑓: 0.13 ( 12552 hom. )

Consequence

LGALS4
NM_006149.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.483

Publications

5 publications found

Variant links:

Genes affected

LGALS4 (HGNC:6565): (galectin 4) The galectins are a family of beta-galactoside-binding proteins implicated in modulating cell-cell and cell-matrix interactions. The expression of this gene is restricted to small intestine, colon, and rectum, and it is underexpressed in colorectal cancer. [provided by RefSeq, Jul 2008]

LGALS4 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LGALS4	NM_006149.4 link	c.45+48G>A		intron_variant	Intron 1 of 9	ENST00000307751.9	NP_006140.1
LGALS4	XM_011526973.3 link	c.45+48G>A		intron_variant	Intron 1 of 8		XP_011525275.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LGALS4	ENST00000307751.9 link	c.45+48G>A		intron_variant	Intron 1 of 9	1	NM_006149.4	ENSP00000302100.3

Frequencies

GnomAD3 genomes

AF:

0.0918

AC:

13961

AN:

152082

Hom.:

851

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0243

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.0908

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.00328

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.0914

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.101

GnomAD2 exomes

AF:

0.118

AC:

28855

AN:

244550

AF XY:

0.126

show subpopulations

Gnomad AFR exome

AF:

0.0215

Gnomad AMR exome

AF:

0.101

Gnomad ASJ exome

AF:

0.126

Gnomad EAS exome

AF:

0.00272

Gnomad FIN exome

AF:

0.0908

Gnomad NFE exome

AF:

0.136

Gnomad OTH exome

AF:

0.131

GnomAD4 exome

AF:

0.126

AC:

182104

AN:

1445578

Hom.:

12552

Cov.:

AF XY:

0.129

AC XY:

92991

AN XY:

719986

show subpopulations

African (AFR)

AF:

0.0215

AC:

715

AN:

33306

American (AMR)

AF:

0.0988

AC:

4408

AN:

44610

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

3228

AN:

25996

East Asian (EAS)

AF:

0.00159

AC:

AN:

39652

South Asian (SAS)

AF:

0.201

AC:

17280

AN:

85944

European-Finnish (FIN)

AF:

0.0929

AC:

4364

AN:

46950

Middle Eastern (MID)

AF:

0.198

AC:

1134

AN:

5734

European-Non Finnish (NFE)

AF:

0.130

AC:

143862

AN:

1103410

Other (OTH)

AF:

0.118

AC:

7050

AN:

59976

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

7741

15482

23224

30965

38706

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5094

10188

15282

20376

25470

<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:

0.0918

AC:

13965

AN:

152200

Hom.:

849

Cov.:

AF XY:

0.0921

AC XY:

6854

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.0242

AC:

1007

AN:

41554

American (AMR)

AF:

0.0909

AC:

1388

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

429

AN:

3470

East Asian (EAS)

AF:

0.00348

AC:

AN:

5178

South Asian (SAS)

AF:

0.200

AC:

966

AN:

4822

European-Finnish (FIN)

AF:

0.0914

AC:

969

AN:

10602

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.129

AC:

8798

AN:

67982

Other (OTH)

AF:

0.102

AC:

215

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

640

1281

1921

2562

3202

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.111

Hom.:

580

Bravo

AF:

0.0866

Asia WGS

AF:

0.0970

AC:

339

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.2

(source)

DANN

Benign

0.48

PhyloP100

0.48

PromoterAI

0.0092

Neutral

(source)

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