GeneBe

rs549043849

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000902330.1(GALT):​c.-28-818_-28-809delTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000080 ( 0 hom., cov: 0)

Consequence

GALT
ENST00000902330.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Publications

0 publications found
Variant links:
Genes affected
GALT (HGNC:4135): (galactose-1-phosphate uridylyltransferase) Galactose-1-phosphate uridyl transferase (GALT) catalyzes the second step of the Leloir pathway of galactose metabolism, namely the conversion of UDP-glucose + galactose-1-phosphate to glucose-1-phosphate + UDP-galactose. The absence of this enzyme results in classic galactosemia in humans and can be fatal in the newborn period if lactose is not removed from the diet. The pathophysiology of galactosemia has not been clearly defined. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
GALT Gene-Disease associations (from GenCC):
  • classic galactosemia
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae)
  • galactosemia
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen, Myriad Women’s Health

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000902330.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt

There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
GALT
ENST00000902330.1
c.-28-818_-28-809delTTTTTTTTTT
intron
N/AENSP00000572389.1
GALT
ENST00000902331.1
c.-28-818_-28-809delTTTTTTTTTT
intron
N/AENSP00000572390.1
GALT
ENST00000902333.1
c.-28-818_-28-809delTTTTTTTTTT
intron
N/AENSP00000572392.1

Frequencies

GnomAD3 genomes
AF:
0.00000796
AC:
1
AN:
125640
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000312
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00000796
AC:
1
AN:
125640
Hom.:
0
Cov.:
0
AF XY:
0.0000168
AC XY:
1
AN XY:
59550
show subpopulations
African (AFR)
AF:
0.0000312
AC:
1
AN:
32020
American (AMR)
AF:
0.00
AC:
0
AN:
12200
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3228
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4244
South Asian (SAS)
AF:
0.00
AC:
0
AN:
3676
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
6078
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
258
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
61392
Other (OTH)
AF:
0.00
AC:
0
AN:
1698
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<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:
0.00
Hom.:
247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs549043849; hg19: chr9-34645845; API