rs9295089
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_054114.5(TAGAP):c.148+657A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,602 control chromosomes in the GnomAD database, including 4,422 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 0.19 ( 4419 hom., cov: 33)
Exomes 𝑓: 0.061 ( 3 hom. )
Consequence
TAGAP
NM_054114.5 intron
NM_054114.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.509
Genes affected
TAGAP (HGNC:15669): (T cell activation RhoGTPase activating protein) This gene encodes a member of the Rho GTPase-activator protein superfamily. The encoded protein may function as a Rho GTPase-activating protein. Alterations in this gene may be associated with several diseases, including rheumatoid arthritis, celiac disease, and multiple sclerosis. Alternate splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2013]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAGAP | NM_054114.5 | c.148+657A>G | intron_variant | ENST00000367066.8 | |||
TAGAP-AS1 | NR_183546.1 | n.1972T>C | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAGAP | ENST00000367066.8 | c.148+657A>G | intron_variant | 1 | NM_054114.5 | P1 | |||
TAGAP-AS1 | ENST00000646912.1 | n.536+624T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.189 AC: 28758AN: 152126Hom.: 4400 Cov.: 33
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GnomAD4 exome AF: 0.0611 AC: 22AN: 360Hom.: 3 Cov.: 0 AF XY: 0.0539 AC XY: 11AN XY: 204
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GnomAD4 genome ? AF: 0.189 AC: 28824AN: 152242Hom.: 4419 Cov.: 33 AF XY: 0.183 AC XY: 13605AN XY: 74454
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ClinVar
Not reported inComputational scores
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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