Variant chr22-24614779-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001288833.2(GGT1):c.168T>C(p.Asp56Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0111 in 1,613,382 control chromosomes in the GnomAD database, including 1,328 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.053 ( 686 hom., cov: 31)

Exomes 𝑓: 0.0067 ( 642 hom. )

Consequence

GGT1
NM_001288833.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.56

Variant links:

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]

GGT1 links:

ENSG00000286070 (HGNC:):

ENSG00000286070 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 22-24614779-T-C is Benign according to our data. Variant chr22-24614779-T-C is described in ClinVar as [Benign]. Clinvar id is 1244940.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GGT1	NM_001288833.2 linkuse as main transcript	c.168T>C	p.Asp56Asp	synonymous_variant	6/16	ENST00000400382.6	NP_001275762.1	P19440-1A0A140VJJ9
GGT1	NM_013421.3 linkuse as main transcript	c.168T>C	p.Asp56Asp	synonymous_variant	7/17		NP_038265.2	P19440-1A0A140VJJ9
GGT1	NM_013430.3 linkuse as main transcript	c.168T>C	p.Asp56Asp	synonymous_variant	6/16		NP_038347.2	P19440-1A0A140VJJ9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
GGT1	ENST00000400382.6 linkuse as main transcript	c.168T>C	p.Asp56Asp	synonymous_variant	6/16	2	NM_001288833.2	ENSP00000383232.1	P19440-1
ENSG00000286070	ENST00000652248.1 linkuse as main transcript	n.*658T>C		non_coding_transcript_exon_variant	10/20			ENSP00000499210.1
ENSG00000286070	ENST00000652248.1 linkuse as main transcript	n.*658T>C		3_prime_UTR_variant	10/20			ENSP00000499210.1

Frequencies

GnomAD3 genomes

AF:

0.0527

AC:

8013

AN:

152026

Hom.:

678

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0237

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0227

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.000765

Gnomad OTH

AF:

0.0427

GnomAD3 exomes

AF:

0.0153

AC:

3797

AN:

247736

Hom.:

267

AF XY:

0.0132

AC XY:

1784

AN XY:

134680

show subpopulations

Gnomad AFR exome

AF:

0.178

Gnomad AMR exome

AF:

0.00975

Gnomad ASJ exome

AF:

0.0000996

Gnomad EAS exome

AF:

0.000168

Gnomad SAS exome

AF:

0.0212

Gnomad FIN exome

AF:

0.0000928

Gnomad NFE exome

AF:

0.000757

Gnomad OTH exome

AF:

0.00997

GnomAD4 exome

AF:

0.00671

AC:

9807

AN:

1461238

Hom.:

642

Cov.:

AF XY:

0.00648

AC XY:

4711

AN XY:

726932

show subpopulations

Gnomad4 AFR exome

AF:

0.184

Gnomad4 AMR exome

AF:

0.0113

Gnomad4 ASJ exome

AF:

0.000306

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0201

Gnomad4 FIN exome

AF:

0.000188

Gnomad4 NFE exome

AF:

0.000449

Gnomad4 OTH exome

AF:

0.0143

GnomAD4 genome

AF:

0.0529

AC:

8045

AN:

152144

Hom.:

686

Cov.:

AF XY:

0.0513

AC XY:

3813

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.179

Gnomad4 AMR

AF:

0.0237

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0223

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.000765

Gnomad4 OTH

AF:

0.0417

Alfa

AF:

0.0243

Hom.:

158

Bravo

AF:

0.0593

EpiCase

AF:

0.00120

EpiControl

AF:

0.00101

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.078

DANN

Benign

0.45

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over