rs13008299
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_199280.4(TOGARAM2):c.1853+757T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,020 control chromosomes in the GnomAD database, including 6,077 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 0.28 ( 6077 hom., cov: 32)
Consequence
TOGARAM2
NM_199280.4 intron
NM_199280.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.340
Genes affected
TOGARAM2 (HGNC:33715): (TOG array regulator of axonemal microtubules 2) Predicted to enable microtubule binding activity. Predicted to be involved in mitotic spindle assembly. Predicted to be active in cilium and microtubule cytoskeleton. [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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOGARAM2 | NM_199280.4 | c.1853+757T>G | intron_variant | ENST00000379558.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOGARAM2 | ENST00000379558.5 | c.1853+757T>G | intron_variant | 5 | NM_199280.4 | P1 | |||
TOGARAM2 | ENST00000401723.5 | c.158+757T>G | intron_variant | 5 | |||||
TOGARAM2 | ENST00000465300.5 | n.588+757T>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.281 AC: 42725AN: 151902Hom.: 6069 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.281 AC: 42752AN: 152020Hom.: 6077 Cov.: 32 AF XY: 0.278 AC XY: 20653AN XY: 74308
GnomAD4 genome
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32
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20653
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74308
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715
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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