Genetic Variant NM_020129.3:c.16-626C>T (chr19-39705971-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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

GnomAD3 exomes

AF:

0.0915

AC:

22758

AN:

248714

Hom.:

1363

AF XY:

0.0912

AC XY:

12274

AN XY:

134628

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 SAS exome

AF:

0.0295

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

Gnomad4 AFR exome

AF:

0.0434

Gnomad4 AMR exome

AF:

0.0660

Gnomad4 ASJ exome

AF:

0.0966

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0314

Gnomad4 FIN exome

AF:

0.163

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.101

GnomAD4 genome

AF:

0.0941

AC:

14327

AN:

152182

Hom.:

825

Cov.:

AF XY:

0.0919

AC XY:

6841

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.0477

Gnomad4 AMR

AF:

0.0904

Gnomad4 ASJ

AF:

0.0964

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0255

Gnomad4 FIN

AF:

0.161

Gnomad4 NFE

AF:

0.125

Gnomad4 OTH

AF:

0.102

Alfa

AF:

0.115

Hom.:

1605

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

BayesDel_addAF

Benign

-0.86

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.1

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

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

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over