rs7317038
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024719.4(GRTP1):c.182-3102G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,978 control chromosomes in the GnomAD database, including 9,227 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 0.34 ( 9227 hom., cov: 34)
Consequence
GRTP1
NM_024719.4 intron
NM_024719.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.217
Genes affected
GRTP1 (HGNC:20310): (growth hormone regulated TBC protein 1) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.95).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRTP1 | NM_024719.4 | c.182-3102G>A | intron_variant | ENST00000375431.9 | |||
GRTP1-AS1 | NR_046541.1 | n.1254+2462C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRTP1 | ENST00000375431.9 | c.182-3102G>A | intron_variant | 1 | NM_024719.4 | P1 | |||
GRTP1 | ENST00000375430.8 | c.182-3102G>A | intron_variant | 1 | |||||
GRTP1-AS1 | ENST00000423246.1 | n.156-2976C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
GRTP1 | ENST00000620217.4 | c.182-3102G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.340 AC: 51694AN: 151860Hom.: 9215 Cov.: 34
GnomAD3 genomes
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34
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.340 AC: 51736AN: 151978Hom.: 9227 Cov.: 34 AF XY: 0.341 AC XY: 25322AN XY: 74266
GnomAD4 genome
?
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51736
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151978
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34
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25322
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74266
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1653
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3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
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