Genetic Variant GALT:c.-28-829_-28-828insTTTT (chr9-34645848-A-ATTTT) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000902330.1(GALT):c.-28-829_-28-828insTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.047 ( 296 hom., cov: 0)

Consequence

GALT
ENST00000902330.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.901

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, Labcorp Genetics (formerly Invitae), Orphanet
galactosemia
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen, Myriad Women's Health

GALT links:

ENSG00000294190 (HGNC:):

ENSG00000294190 links:

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new If you want to explore the variant's impact on the transcript ENST00000902330.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 9-34645848-A-ATTTT is Benign according to our data. Variant chr9-34645848-A-ATTTT is described in ClinVar as Benign. ClinVar VariationId is 1331426.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

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.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
GALT	ENST00000902330.1	c.-28-829_-28-828insTTTT	intron	N/A	ENSP00000572389.1
GALT	ENST00000902331.1	c.-28-829_-28-828insTTTT	intron	N/A	ENSP00000572390.1
GALT	ENST00000902333.1	c.-28-829_-28-828insTTTT	intron	N/A	ENSP00000572392.1

Frequencies

GnomAD3 genomes

AF:

0.0467

AC:

5864

AN:

125572

Hom.:

296

Cov.:

show subpopulations

Gnomad AFR

AF:

0.104

Gnomad AMI

AF:

0.0865

Gnomad AMR

AF:

0.0552

Gnomad ASJ

AF:

0.00620

Gnomad EAS

AF:

0.0627

Gnomad SAS

AF:

0.0201

Gnomad FIN

AF:

0.0357

Gnomad MID

AF:

0.0116

Gnomad NFE

AF:

0.0187

Gnomad OTH

AF:

0.0371

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0467

AC:

5861

AN:

125550

Hom.:

296

Cov.:

AF XY:

0.0478

AC XY:

2843

AN XY:

59516

show subpopulations

African (AFR)

AF:

0.104

AC:

3328

AN:

32020

American (AMR)

AF:

0.0552

AC:

673

AN:

12202

Ashkenazi Jewish (ASJ)

AF:

0.00620

AC:

AN:

3228

East Asian (EAS)

AF:

0.0629

AC:

266

AN:

4228

South Asian (SAS)

AF:

0.0203

AC:

AN:

3654

European-Finnish (FIN)

AF:

0.0357

AC:

217

AN:

6070

Middle Eastern (MID)

AF:

0.0127

AC:

AN:

236

European-Non Finnish (NFE)

AF:

0.0186

AC:

1144

AN:

61362

Other (OTH)

AF:

0.0369

AC:

AN:

1706

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

233

466

699

932

1165

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

198

264

330

<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:

0.0184

Hom.:

247

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.90

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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9-34645848-ATTTTTTTTTT-ATTTTTTTTTTTTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over