9-34645685-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000605275.1(GALT):n.209-976dup variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 137,474 control chromosomes in the GnomAD database, including 992 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (992 hom., cov: 27)
• Consequence: GALT ENST00000605275.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.520

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 9-34645685-C-CT is Benign according to our data. Variant chr9-34645685-C-CT is described in ClinVar as [Benign]. Clinvar id is 1331423.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALT	ENST00000605275.1	n.209-976dup		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 15258 AN: 137468 Hom.: 994 Cov.: 27

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.111 AC: 15257 AN: 137474 Hom.: 992 Cov.: 27 AF XY: 0.110 AC XY: 7265 AN XY: 66292

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0856

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0519

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.0911

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.105

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Dec 16, 2021

Variant summary: GALT c.-1004dupT is located in the untranscribed region upstream of the GALT gene. The variant allele was found at a frequency of 0.1 in 23774 control chromosomes in the gnomAD database, including 156 homozygotes. The observed variant frequency is approximately 36-fold of the estimated maximal expected allele frequency for a pathogenic variant in GALT causing Galactosemia phenotype (0.0029), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.-1004dupT in individuals affected with Galactosemia and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201344398; hg19: chr9-34645682;