dbSNP rs3962697: 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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GGT2P	NR_172944.1 link	n.2200+29C>G		intron_variant	Intron 13 of 14

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
GGT2P	ENST00000697421.1 link	n.1419+29C>G	intron_variant	Intron 10 of 11
ENSG00000290983	ENST00000697422.1 link	n.2391+29C>G	intron_variant	Intron 12 of 13
ENSG00000290983	ENST00000806875.1 link	n.1136+29C>G	intron_variant	Intron 7 of 8

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over