Genetic Variant GGT2P:n.1419+29C>G (chr22-21208755-G-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000697421.1(GGT2P):n.1419+29C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.000020 ( 0 hom., cov: 4)

Exomes 𝑓: 0.000048 ( 7 hom. )

Failed GnomAD Quality Control

Consequence

GGT2P
ENST00000697421.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.142

Publications

1 publications found

Variant links:

Genes affected

GGT2P (HGNC:4251): (gamma-glutamyltransferase 2, pseudogene) This gene (GGT2P) appears to be a human duplication of the gamma-glutamyltransferase 1 (GGT1) gene. While GGT2P and GGT1 can potentially encode proteins of the same size and with 94% identity, the ability of GGT2P to encode a stable, functional enzyme has been disputed (see PMID:23682772). Since it is also expressed at a much lower level than GGT1, GGT2P is now thought to be a processed pseudogene. [provided by RefSeq, Jan 2022]

GGT2P links:

ENSG00000290983 (HGNC:):

ENSG00000290983 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697421.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GGT2P	NR_172944.1		n.2200+29C>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
GGT2P	ENST00000697421.1	n.1419+29C>G	intron	N/A
ENSG00000290983	ENST00000697422.1	n.2391+29C>G	intron	N/A
ENSG00000290983	ENST00000806875.1	n.1136+29C>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0000205

AC:

AN:

48822

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000490

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000332

AC:

AN:

60178

AF XY:

0.0000325

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000764

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000482

AC:

AN:

788748

Hom.:

Cov.:

AF XY:

0.0000517

AC XY:

AN XY:

405808

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24904

American (AMR)

AF:

0.00

AC:

AN:

34742

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18980

East Asian (EAS)

AF:

0.00

AC:

AN:

23264

South Asian (SAS)

AF:

0.00

AC:

AN:

60402

European-Finnish (FIN)

AF:

0.0000247

AC:

AN:

40468

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2706

European-Non Finnish (NFE)

AF:

0.0000602

AC:

AN:

547984

Other (OTH)

AF:

0.000113

AC:

AN:

35298

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000205

AC:

AN:

48822

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

22724

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

18682

American (AMR)

AF:

0.00

AC:

AN:

3978

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1008

East Asian (EAS)

AF:

0.00

AC:

AN:

482

South Asian (SAS)

AF:

0.00

AC:

AN:

660

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2564

Middle Eastern (MID)

AF:

0.00

AC:

AN:

126

European-Non Finnish (NFE)

AF:

0.0000490

AC:

AN:

20426

Other (OTH)

AF:

0.00

AC:

AN:

630

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.5

(source)

DANN

Benign

0.69

PhyloP100

0.14

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over