rs846910
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NR_134510.1(HSD11B1-AS1):n.67-38848T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
Consequence
HSD11B1-AS1
NR_134510.1 intron, non_coding_transcript
NR_134510.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.855
Genes affected
HSD11B1-AS1 (HGNC:54053): (HSD11B1 antisense RNA 1)
HSD11B1 (HGNC:5208): (hydroxysteroid 11-beta dehydrogenase 1) The protein encoded by this gene is a microsomal enzyme that catalyzes the conversion of the stress hormone cortisol to the inactive metabolite cortisone. In addition, the encoded protein can catalyze the reverse reaction, the conversion of cortisone to cortisol. Too much cortisol can lead to central obesity, and a particular variation in this gene has been associated with obesity and insulin resistance in children. Mutations in this gene and H6PD (hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)) are the cause of cortisone reductase deficiency. Alternate splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, May 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSD11B1-AS1 | NR_134510.1 | n.67-38848T>G | intron_variant, non_coding_transcript_variant | ||||
HSD11B1 | NM_001206741.2 | c.-48-2986A>C | intron_variant | ||||
HSD11B1 | NM_181755.3 | c.-26-3008A>C | intron_variant | ||||
HSD11B1-AS1 | NR_134509.1 | n.96+22121T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD11B1-AS1 | ENST00000441672.1 | n.96+22121T>G | intron_variant, non_coding_transcript_variant | 3 | |||||
HSD11B1 | ENST00000261465.5 | c.-48-2986A>C | intron_variant | 5 | |||||
HSD11B1 | ENST00000367028.6 | c.-48-2986A>C | intron_variant | 5 | P1 | ||||
HSD11B1 | ENST00000615289.4 | c.-26-3008A>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at