NM_020129.3:c.199T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020129.3(LGALS14):​c.199T>C​(p.Cys67Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 1,613,706 control chromosomes in the GnomAD database, including 365,681 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C67Y) has been classified as Uncertain significance.

Frequency

Genomes: š‘“ 0.68 ( 36082 hom., cov: 32)
Exomes š‘“: 0.67 ( 329599 hom. )

Consequence

LGALS14
NM_020129.3 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.202
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]

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=1.9925528E-6).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LGALS14NM_020129.3 linkc.199T>C p.Cys67Arg missense_variant Exon 3 of 4 ENST00000392052.8 NP_064514.1 Q8TCE9-1
LGALS14NM_203471.2 linkc.286T>C p.Cys96Arg missense_variant Exon 4 of 5 NP_982297.1 Q8TCE9-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LGALS14ENST00000392052.8 linkc.199T>C p.Cys67Arg missense_variant Exon 3 of 4 1 NM_020129.3 ENSP00000375905.2 Q8TCE9-1
LGALS14ENST00000360675.7 linkc.286T>C p.Cys96Arg missense_variant Exon 4 of 5 3 ENSP00000353893.2 Q8TCE9-2
LGALS14ENST00000601802.1 linkc.148T>C p.Cys50Arg missense_variant Exon 2 of 3 5 ENSP00000471660.1 M0R163

Frequencies

GnomAD3 genomes
AF:
0.681
AC:
103507
AN:
151986
Hom.:
36035
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.787
Gnomad AMI
AF:
0.576
Gnomad AMR
AF:
0.507
Gnomad ASJ
AF:
0.699
Gnomad EAS
AF:
0.363
Gnomad SAS
AF:
0.693
Gnomad FIN
AF:
0.695
Gnomad MID
AF:
0.620
Gnomad NFE
AF:
0.679
Gnomad OTH
AF:
0.642
GnomAD3 exomes
AF:
0.626
AC:
157061
AN:
251074
Hom.:
51812
AF XY:
0.636
AC XY:
86246
AN XY:
135682
show subpopulations
Gnomad AFR exome
AF:
0.795
Gnomad AMR exome
AF:
0.392
Gnomad ASJ exome
AF:
0.698
Gnomad EAS exome
AF:
0.342
Gnomad SAS exome
AF:
0.700
Gnomad FIN exome
AF:
0.692
Gnomad NFE exome
AF:
0.679
Gnomad OTH exome
AF:
0.637
GnomAD4 exome
AF:
0.667
AC:
974471
AN:
1461602
Hom.:
329599
Cov.:
46
AF XY:
0.668
AC XY:
486026
AN XY:
727122
show subpopulations
Gnomad4 AFR exome
AF:
0.801
Gnomad4 AMR exome
AF:
0.409
Gnomad4 ASJ exome
AF:
0.697
Gnomad4 EAS exome
AF:
0.397
Gnomad4 SAS exome
AF:
0.700
Gnomad4 FIN exome
AF:
0.695
Gnomad4 NFE exome
AF:
0.678
Gnomad4 OTH exome
AF:
0.661
GnomAD4 genome
AF:
0.681
AC:
103597
AN:
152104
Hom.:
36082
Cov.:
32
AF XY:
0.676
AC XY:
50286
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.788
Gnomad4 AMR
AF:
0.506
Gnomad4 ASJ
AF:
0.699
Gnomad4 EAS
AF:
0.364
Gnomad4 SAS
AF:
0.693
Gnomad4 FIN
AF:
0.695
Gnomad4 NFE
AF:
0.679
Gnomad4 OTH
AF:
0.638
Alfa
AF:
0.666
Hom.:
85525
Bravo
AF:
0.665
TwinsUK
AF:
0.688
AC:
2551
ALSPAC
AF:
0.691
AC:
2662
ESP6500AA
AF:
0.786
AC:
3465
ESP6500EA
AF:
0.674
AC:
5793
ExAC
AF:
0.642
AC:
77913
Asia WGS
AF:
0.541
AC:
1883
AN:
3478
EpiCase
AF:
0.667
EpiControl
AF:
0.664

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.039
BayesDel_addAF
Benign
-0.85
T
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.39
DANN
Benign
0.10
DEOGEN2
Benign
0.0044
T;.
Eigen
Benign
-1.7
Eigen_PC
Benign
-1.7
FATHMM_MKL
Benign
0.000060
N
LIST_S2
Benign
0.19
T;T
MetaRNN
Benign
0.0000020
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-1.7
N;.
PrimateAI
Benign
0.32
T
PROVEAN
Benign
3.3
N;N
REVEL
Benign
0.022
Sift
Benign
0.99
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.0
B;.
Vest4
0.046
MPC
0.18
ClinPred
0.00085
T
GERP RS
1.1
Varity_R
0.23
gMVP
0.43

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

LitVar

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

Other links and lift over

dbSNP: rs4830; hg19: chr19-40197924; COSMIC: COSV62372292; API