rs7918118
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012341.3(GTPBP4):c.461-325C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 291,188 control chromosomes in the GnomAD database, including 84,649 homozygotes. 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 0.77 ( 45140 hom., cov: 31)
Exomes 𝑓: 0.75 ( 39509 hom. )
Consequence
GTPBP4
NM_012341.3 intron
NM_012341.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.155
Genes affected
GTPBP4 (HGNC:21535): (GTP binding protein 4) GTP-binding proteins are GTPases and function as molecular switches that can flip between two states: active, when GTP is bound, and inactive, when GDP is bound. 'Active' in this context usually means that the molecule acts as a signal to trigger other events in the cell. When an extracellular ligand binds to a G-protein-linked receptor, the receptor changes its conformation and switches on the trimeric G proteins that associate with it by causing them to eject their GDP and replace it with GTP. The switch is turned off when the G protein hydrolyzes its own bound GTP, converting it back to GDP. But before that occurs, the active protein has an opportunity to diffuse away from the receptor and deliver its message for a prolonged period to its downstream target. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTPBP4 | NM_012341.3 | c.461-325C>A | intron_variant | ENST00000360803.9 | |||
GTPBP4 | XM_047424932.1 | c.320-325C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTPBP4 | ENST00000360803.9 | c.461-325C>A | intron_variant | 1 | NM_012341.3 | P1 | |||
GTPBP4 | ENST00000360059.5 | c.320-325C>A | intron_variant | 5 | |||||
GTPBP4 | ENST00000491635.1 | n.1015C>A | non_coding_transcript_exon_variant | 3/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.767 AC: 116579AN: 151972Hom.: 45096 Cov.: 31
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GnomAD4 exome AF: 0.750 AC: 104334AN: 139098Hom.: 39509 Cov.: 0 AF XY: 0.754 AC XY: 55687AN XY: 73812
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GnomAD4 genome ? AF: 0.767 AC: 116678AN: 152090Hom.: 45140 Cov.: 31 AF XY: 0.773 AC XY: 57519AN XY: 74374
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at