rs1062177
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005754.3(G3BP1):c.*1049C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,470 control chromosomes in the GnomAD database, including 3,716 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 0.20 ( 3692 hom., cov: 32)
Exomes 𝑓: 0.34 ( 24 hom. )
Consequence
G3BP1
NM_005754.3 3_prime_UTR
NM_005754.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.222
Genes affected
G3BP1 (HGNC:30292): (G3BP stress granule assembly factor 1) This gene encodes one of the DNA-unwinding enzymes which prefers partially unwound 3'-tailed substrates and can also unwind partial RNA/DNA and RNA/RNA duplexes in an ATP-dependent fashion. This enzyme is a member of the heterogeneous nuclear RNA-binding proteins and is also an element of the Ras signal transduction pathway. It binds specifically to the Ras-GTPase-activating protein by associating with its SH3 domain. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [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=-0.82).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
G3BP1 | NM_005754.3 | c.*1049C>T | 3_prime_UTR_variant | 12/12 | ENST00000356245.8 | ||
G3BP1 | NM_198395.2 | c.*1049C>T | 3_prime_UTR_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G3BP1 | ENST00000356245.8 | c.*1049C>T | 3_prime_UTR_variant | 12/12 | 1 | NM_005754.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.197 AC: 29921AN: 151924Hom.: 3695 Cov.: 32
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GnomAD4 exome AF: 0.342 AC: 147AN: 430Hom.: 24 Cov.: 0 AF XY: 0.326 AC XY: 84AN XY: 258
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GnomAD4 genome ? AF: 0.197 AC: 29909AN: 152040Hom.: 3692 Cov.: 32 AF XY: 0.203 AC XY: 15075AN XY: 74314
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ClinVar
Not reported inComputational scores
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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