rs11157552
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_148361.1(TRD-AS1):n.226-1022A>G 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 0.799 in 150,640 control chromosomes in the GnomAD database, including 48,643 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 0.80 ( 48643 hom., cov: 25)
Consequence
TRD-AS1
NR_148361.1 intron, non_coding_transcript
NR_148361.1 intron, non_coding_transcript
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.413
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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRD-AS1 | NR_148361.1 | n.226-1022A>G | intron_variant, non_coding_transcript_variant | ||||
TRD-AS1 | NR_148362.1 | n.290-1022A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRD-AS1 | ENST00000656379.1 | n.270+17617A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.799 AC: 120197AN: 150522Hom.: 48593 Cov.: 25
GnomAD3 genomes
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25
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.799 AC: 120306AN: 150640Hom.: 48643 Cov.: 25 AF XY: 0.795 AC XY: 58417AN XY: 73506
GnomAD4 genome
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73506
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at