22-24595896-C-T

Position:

• chr22-24595896-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013430.3(GGT1):​c.-428-12058C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,174 control chromosomes in the GnomAD database, including 8,050 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8050 hom., cov: 33)
• Consequence: GGT1 NM_013430.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

Genes affected

GGT1 (HGNC:4250): (gamma-glutamyltransferase 1) The enzyme encoded by this gene is a type I gamma-glutamyltransferase that catalyzes the transfer of the glutamyl moiety of glutathione to a variety of amino acids and dipeptide acceptors. The enzyme is composed of a heavy chain and a light chain, which are derived from a single precursor protein. It is expressed in tissues involved in absorption and secretion and may contribute to the etiology of diabetes and other metabolic disorders. Multiple alternatively spliced variants have been identified. There are a number of related genes present on chromosomes 20 and 22, and putative pseudogenes for this gene on chromosomes 2, 13, and 22. [provided by RefSeq, Jan 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GGT1	NM_013430.3	c.-428-12058C>T		intron_variant			NP_038347.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GGT1	ENST00000411974.5	c.-324+1010C>T		intron_variant		3		ENSP00000389935
GGT1	ENST00000456869.5	c.-432+1010C>T		intron_variant		3		ENSP00000415129

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48311 AN: 152056 Hom.: 8042 Cov.: 33

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.318 AC: 48357 AN: 152174 Hom.: 8050 Cov.: 33 AF XY: 0.313 AC XY: 23249 AN XY: 74396

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.331

Alfa AF: 0.286 Hom.: 3416

Bravo AF: 0.338

Asia WGS AF: 0.229 AC: 794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6519519; hg19: chr22-24991863; COSMIC: COSV50646223; COSMIC: COSV50646223;