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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006149.4. 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
	LGALS4	NM_006149.4	MANE Select	c.45+48G>A		intron	N/A	NP_006140.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LGALS4	ENST00000307751.9	TSL:1 MANE Select	c.45+48G>A	intron	N/A	ENSP00000302100.3
LGALS4	ENST00000594209.1	TSL:2	c.-320G>A	5_prime_UTR	Exon 1 of 2	ENSP00000472990.1
LGALS4	ENST00000955359.1		c.45+48G>A	intron	N/A	ENSP00000625418.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over