chr9-34645685-C-CTT

Variant names:

• chr9-34645685-C-CTT
• rs201344398
• ENST00000902330.1:c.-28-977_-28-976dupTT

Variant summary

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

The ENST00000902330.1(GALT):​c.-28-977_-28-976dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0276 in 137,514 control chromosomes in the GnomAD database, including 215 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.028 (215 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-CTT is Benign according to our data. Variant chr9-34645685-C-CTT is described in ClinVar as Benign. ClinVar VariationId is 1677034.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0921 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.-28-977_-28-976dupTT		intron	N/A	ENSP00000572389.1
	GALT	ENST00000902331.1		c.-28-977_-28-976dupTT		intron	N/A	ENSP00000572390.1
	GALT	ENST00000902333.1		c.-28-977_-28-976dupTT		intron	N/A	ENSP00000572392.1

Frequencies

GnomAD3 genomes AF: 0.0276 AC: 3791 AN: 137508 Hom.: 215 Cov.: 27

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0127

Gnomad ASJ AF: 0.00275

Gnomad EAS AF: 0.000417

Gnomad SAS AF: 0.00256

Gnomad FIN AF: 0.00114

Gnomad MID AF: 0.00699

Gnomad NFE AF: 0.00113

Gnomad OTH AF: 0.0223

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

GnomAD4 genome AF: 0.0276 AC: 3796 AN: 137514 Hom.: 215 Cov.: 27 AF XY: 0.0266 AC XY: 1765 AN XY: 66306

African (AFR) AF: 0.0947 AC: 3477 AN: 36704

American (AMR) AF: 0.0126 AC: 174 AN: 13762

Ashkenazi Jewish (ASJ) AF: 0.00275 AC: 9 AN: 3268

East Asian (EAS) AF: 0.000418 AC: 2 AN: 4780

South Asian (SAS) AF: 0.00257 AC: 11 AN: 4280

European-Finnish (FIN) AF: 0.00114 AC: 9 AN: 7914

Middle Eastern (MID) AF: 0.00379 AC: 1 AN: 264

European-Non Finnish (NFE) AF: 0.00113 AC: 72 AN: 63812

Other (OTH) AF: 0.0221 AC: 41 AN: 1854

Alfa AF: 0.00 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;