dbSNP rs35541195: LGALS14:c.16-626C>T (chr19-39705971-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_020129.3(LGALS14):c.16-626C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,613,500 control chromosomes in the GnomAD database, including 11,127 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 0.094 ( 825 hom., cov: 32)

Exomes 𝑓: 0.11 ( 10302 hom. )

Consequence

LGALS14
NM_020129.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.379

Publications

9 publications found

Variant links:

Genes affected

LGALS14 (HGNC:30054): (galectin 14) This gene is predominantly expressed in placenta. The encoded protein belongs to the galectin (galaptin/S-lectin) family. The members of galectin family contain one or two carbohydrate recognition domains, which can bind beta-galactoside. Two alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

LGALS14 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 (MetaRNN=0.0016011596).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LGALS14	NM_020129.3 link	c.16-626C>T		intron_variant	Intron 1 of 3	ENST00000392052.8	NP_064514.1	Q8TCE9-1
LGALS14	NM_203471.2 link	c.64C>T	p.Arg22Cys	missense_variant	Exon 2 of 5		NP_982297.1	Q8TCE9-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
LGALS14	ENST00000392052.8 link	c.16-626C>T		intron_variant	Intron 1 of 3	1	NM_020129.3	ENSP00000375905.2	Q8TCE9-1
LGALS14	ENST00000360675.7 link	c.64C>T	p.Arg22Cys	missense_variant	Exon 2 of 5	3		ENSP00000353893.2	Q8TCE9-2
LGALS14	ENST00000601802.1 link	c.42-1207C>T		intron_variant	Intron 1 of 2	5		ENSP00000471660.1	M0R163

Frequencies

GnomAD3 genomes

AF:

0.0942

AC:

14323

AN:

152064

Hom.:

825

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0478

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.0906

Gnomad ASJ

AF:

0.0964

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.0249

Gnomad FIN

AF:

0.161

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.102

GnomAD2 exomes

AF:

0.0915

AC:

22758

AN:

248714

AF XY:

0.0912

show subpopulations

Gnomad AFR exome

AF:

0.0464

Gnomad AMR exome

AF:

0.0632

Gnomad ASJ exome

AF:

0.0975

Gnomad EAS exome

AF:

0.000109

Gnomad FIN exome

AF:

0.166

Gnomad NFE exome

AF:

0.123

Gnomad OTH exome

AF:

0.116

GnomAD4 exome

AF:

0.113

AC:

164918

AN:

1461318

Hom.:

10302

Cov.:

AF XY:

0.111

AC XY:

80619

AN XY:

727006

show subpopulations

African (AFR)

AF:

0.0434

AC:

1453

AN:

33462

American (AMR)

AF:

0.0660

AC:

2953

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.0966

AC:

2525

AN:

26128

East Asian (EAS)

AF:

0.000101

AC:

AN:

39688

South Asian (SAS)

AF:

0.0314

AC:

2711

AN:

86246

European-Finnish (FIN)

AF:

0.163

AC:

8728

AN:

53402

Middle Eastern (MID)

AF:

0.0845

AC:

486

AN:

5754

European-Non Finnish (NFE)

AF:

0.126

AC:

139939

AN:

1111562

Other (OTH)

AF:

0.101

AC:

6119

AN:

60358

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

7464

14928

22391

29855

37319

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4870

9740

14610

19480

24350

<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:

0.0941

AC:

14327

AN:

152182

Hom.:

825

Cov.:

AF XY:

0.0919

AC XY:

6841

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0477

AC:

1981

AN:

41526

American (AMR)

AF:

0.0904

AC:

1382

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0964

AC:

334

AN:

3466

East Asian (EAS)

AF:

0.00116

AC:

AN:

5178

South Asian (SAS)

AF:

0.0255

AC:

123

AN:

4818

European-Finnish (FIN)

AF:

0.161

AC:

1702

AN:

10604

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.125

AC:

8516

AN:

67988

Other (OTH)

AF:

0.102

AC:

215

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

671

1342

2014

2685

3356

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

158

316

474

632

790

<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:

0.110

Hom.:

2207

Bravo

AF:

0.0874

TwinsUK

AF:

0.117

AC:

433

ALSPAC

AF:

0.129

AC:

498

ESP6500AA

AF:

0.0542

AC:

239

ESP6500EA

AF:

0.128

AC:

1098

ExAC

AF:

0.0896

AC:

10877

Asia WGS

AF:

0.0210

AC:

AN:

3478

EpiCase

AF:

0.134

EpiControl

AF:

0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.86

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.1

(source)

DANN

Benign

0.84

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.0088

LIST_S2

Benign

0.37

MetaRNN

Benign

0.0016

MetaSVM

Benign

-0.95

PhyloP100

-0.38

PROVEAN

Benign

-0.22

REVEL

Benign

0.040

Sift

Benign

0.056

Sift4G

Uncertain

0.057

Vest4

0.046

MPC

0.14

ClinPred

0.0056

GERP RS

-0.46

gMVP

0.53

Mutation Taster

=100/0

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