chr15-49170353-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002044.4(GALK2):​c.31G>T​(p.Val11Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000625 in 1,440,712 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000062 ( 0 hom. )

Consequence

GALK2
NM_002044.4 missense

Scores

3
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.111
Variant links:
Genes affected
GALK2 (HGNC:4119): (galactokinase 2) This gene encodes a highly efficient N-acetylgalactosamine (GalNAc) kinase, which has galactokinase activity when galactose is present at high concentrations. The encoded protein is a member of the GHMP kinase family. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GALK2NM_002044.4 linkuse as main transcriptc.31G>T p.Val11Phe missense_variant 1/10 ENST00000560031.6 NP_002035.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GALK2ENST00000560031.6 linkuse as main transcriptc.31G>T p.Val11Phe missense_variant 1/101 NM_002044.4 ENSP00000453129 P1Q01415-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.0000189
AC:
4
AN:
212048
Hom.:
0
AF XY:
0.0000263
AC XY:
3
AN XY:
114032
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000633
Gnomad SAS exome
AF:
0.0000761
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000106
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000625
AC:
9
AN:
1440712
Hom.:
0
Cov.:
30
AF XY:
0.00000840
AC XY:
6
AN XY:
714010
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000364
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000272
Gnomad4 OTH exome
AF:
0.0000503
GnomAD4 genome
Cov.:
31
Alfa
AF:
0.0000434
Hom.:
0
Bravo
AF:
0.0000113
ExAC
AF:
0.0000415
AC:
5

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsFeb 27, 2024The c.31G>T (p.V11F) alteration is located in exon 1 (coding exon 1) of the GALK2 gene. This alteration results from a G to T substitution at nucleotide position 31, causing the valine (V) at amino acid position 11 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.095
BayesDel_addAF
Benign
-0.068
T
BayesDel_noAF
Benign
-0.15
CADD
Benign
17
DANN
Uncertain
0.98
DEOGEN2
Benign
0.13
T
Eigen
Benign
-0.60
Eigen_PC
Benign
-0.72
FATHMM_MKL
Benign
0.44
N
LIST_S2
Benign
0.70
T
M_CAP
Benign
0.037
D
MetaRNN
Benign
0.13
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.3
L
MutationTaster
Benign
0.83
D;D;D;D;D
PrimateAI
Benign
0.43
T
PROVEAN
Benign
-1.6
N
Sift
Uncertain
0.0080
D
Sift4G
Uncertain
0.017
D
Polyphen
0.94
P
Vest4
0.25
MutPred
0.25
Loss of loop (P = 0.0112);
MVP
0.75
MPC
0.087
ClinPred
0.14
T
GERP RS
-1.6
Varity_R
0.31
gMVP
0.85

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.23
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.23
Position offset: 5

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: rs750741381; hg19: chr15-49462550; API