9-34645685-CTTTTTTT-CTTTTTTTT

Variant names:

• chr9-34645685-C-CT
• rs201344398
• ENST00000902330.1:c.-28-976dupT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000902330.1(GALT):​c.-28-976dupT variant causes a intron 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 ENST00000902330.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.520
• Publications: 0 publications found

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

ENSG00000294190 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALT	ENST00000902330.1		c.-28-976dupT		intron	N/A	ENSP00000572389.1
	GALT	ENST00000902331.1		c.-28-976dupT		intron	N/A	ENSP00000572390.1
	GALT	ENST00000902333.1		c.-28-976dupT		intron	N/A	ENSP00000572392.1

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

African (AFR) AF: 0.137 AC: 5029 AN: 36700

American (AMR) AF: 0.0856 AC: 1178 AN: 13758

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 404 AN: 3268

East Asian (EAS) AF: 0.0519 AC: 248 AN: 4780

South Asian (SAS) AF: 0.194 AC: 829 AN: 4274

European-Finnish (FIN) AF: 0.0911 AC: 720 AN: 7904

Middle Eastern (MID) AF: 0.117 AC: 31 AN: 264

European-Non Finnish (NFE) AF: 0.101 AC: 6425 AN: 63792

Other (OTH) AF: 0.105 AC: 196 AN: 1858

Alfa AF: 0.0256 Hom.: 33

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs201344398; hg19: chr9-34645682;