rs9268005
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_136245.1(TSBP1-AS1):n.242+1197C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,940 control chromosomes in the GnomAD database, including 35,807 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 0.69 ( 35807 hom., cov: 32)
Consequence
TSBP1-AS1
NR_136245.1 intron, non_coding_transcript
NR_136245.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.854
Genes affected
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSBP1-AS1 | NR_136245.1 | n.242+1197C>A | intron_variant, non_coding_transcript_variant | ||||
TSBP1-AS1 | NR_136244.1 | n.242+1197C>A | intron_variant, non_coding_transcript_variant | ||||
TSBP1-AS1 | NR_136246.1 | n.242+1197C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSBP1-AS1 | ENST00000645134.1 | n.87+1197C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.685 AC: 103996AN: 151822Hom.: 35773 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 genome ? AF: 0.685 AC: 104079AN: 151940Hom.: 35807 Cov.: 32 AF XY: 0.683 AC XY: 50754AN XY: 74258
GnomAD4 genome
?
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151940
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32
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74258
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at