Genetic Variant GALT:c.-28-619_-28-618delAG (chr9-34646057-AAG-A) – 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.-28-619_-28-618delAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0283 in 149,316 control chromosomes in the GnomAD database, including 97 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.028 ( 97 hom., cov: 31)

Consequence

GALT
ENST00000902330.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0250

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

GALT links:

ENSG00000294190 (HGNC:):

ENSG00000294190 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP6

Variant 9-34646057-AAG-A is Benign according to our data. Variant chr9-34646057-AAG-A is described in ClinVar as Benign. ClinVar VariationId is 1331459.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0946 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.-28-619_-28-618delAG	intron	N/A	ENSP00000572389.1
GALT	ENST00000902331.1	c.-28-619_-28-618delAG	intron	N/A	ENSP00000572390.1
GALT	ENST00000902333.1	c.-28-619_-28-618delAG	intron	N/A	ENSP00000572392.1

Frequencies

GnomAD3 genomes

AF:

0.0283

AC:

4226

AN:

149236

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0118

Gnomad AMI

AF:

0.0639

Gnomad AMR

AF:

0.0230

Gnomad ASJ

AF:

0.0598

Gnomad EAS

AF:

0.00156

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.0461

Gnomad MID

AF:

0.0478

Gnomad NFE

AF:

0.0314

Gnomad OTH

AF:

0.0357

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

GnomAD4 genome

AF:

0.0283

AC:

4224

AN:

149316

Hom.:

Cov.:

AF XY:

0.0296

AC XY:

2155

AN XY:

72806

show subpopulations

African (AFR)

AF:

0.0118

AC:

483

AN:

40880

American (AMR)

AF:

0.0229

AC:

343

AN:

14956

Ashkenazi Jewish (ASJ)

AF:

0.0598

AC:

206

AN:

3442

East Asian (EAS)

AF:

0.00156

AC:

AN:

5130

South Asian (SAS)

AF:

0.102

AC:

482

AN:

4720

European-Finnish (FIN)

AF:

0.0461

AC:

453

AN:

9836

Middle Eastern (MID)

AF:

0.0445

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0314

AC:

2106

AN:

67118

Other (OTH)

AF:

0.0354

AC:

AN:

2034

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

200

400

599

799

999

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

174

232

290

<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:

0.00755

Hom.:

Bravo

AF:

0.0234

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

-0.025

Splicing

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

Publications

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9-34646057-AAGAGAG-AAGAG

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