22-24614614-CA-C

Position:

• chr22-24614614-CA-C

Variant summary

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

The NM_001288833.2(GGT1):​c.165-145del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 68,550 control chromosomes in the GnomAD database, including 500 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (500 hom., cov: 29)
• Consequence: GGT1 NM_001288833.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.27

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 -10 ACMG points.

• BP6: Variant 22-24614614-CA-C is Benign according to our data. Variant chr22-24614614-CA-C is described in ClinVar as [Benign]. Clinvar id is 1294465.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GGT1	NM_001288833.2	c.165-145del		intron_variant		ENST00000400382.6
GGT1	NM_013421.3	c.165-145del		intron_variant
GGT1	NM_013430.3	c.165-145del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GGT1	ENST00000400382.6	c.165-145del		intron_variant		2	NM_001288833.2	P1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 7482 AN: 68534 Hom.: 499 Cov.: 29

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.0310

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.0594

Gnomad FIN AF: 0.00413

Gnomad MID AF: 0.0610

Gnomad NFE AF: 0.0125

Gnomad OTH AF: 0.0962

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

GnomAD4 genome AF: 0.109 AC: 7493 AN: 68550 Hom.: 500 Cov.: 29 AF XY: 0.109 AC XY: 3489 AN XY: 32136

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.0745

Gnomad4 ASJ AF: 0.0310

Gnomad4 EAS AF: 0.0190

Gnomad4 SAS AF: 0.0605

Gnomad4 FIN AF: 0.00413

Gnomad4 NFE AF: 0.0125

Gnomad4 OTH AF: 0.0956

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 07, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs4049879; hg19: chr22-25010581;