rs3962697
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NR_172944.1(GGT2P):n.2200+29C>G variant causes a intron, non coding transcript 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
NR_172944.1 intron, non_coding_transcript
NR_172944.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.142
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GGT2P | NR_172944.1 | n.2200+29C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GGT2P | ENST00000697421.1 | n.1419+29C>G | intron_variant, non_coding_transcript_variant | ||||||
ENST00000697422.1 | n.2391+29C>G | intron_variant, non_coding_transcript_variant | |||||||
ENST00000697143.1 | downstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 1AN: 48822Hom.: 0 Cov.: 4 FAILED QC
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GnomAD3 exomes AF: 0.0000332 AC: 2AN: 60178Hom.: 0 AF XY: 0.0000325 AC XY: 1AN XY: 30768
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000482 AC: 38AN: 788748Hom.: 7 Cov.: 11 AF XY: 0.0000517 AC XY: 21AN XY: 405808
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000205 AC: 1AN: 48822Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0AN XY: 22724
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at