1-209687323-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_134510.1(HSD11B1-AS1):​n.67-24262A>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 0.771 in 152,094 control chromosomes in the GnomAD database, including 46,530 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 0.77 ( 46530 hom., cov: 32)

Consequence

HSD11B1-AS1
NR_134510.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.26
Variant links:
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HSD11B1-AS1NR_134510.1 linkuse as main transcriptn.67-24262A>G intron_variant, non_coding_transcript_variant
HSD11B1NM_001206741.2 linkuse as main transcriptc.-49+1038T>C intron_variant
HSD11B1NM_181755.3 linkuse as main transcriptc.-27+1038T>C intron_variant
HSD11B1-AS1NR_134509.1 linkuse as main transcriptn.97-24262A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HSD11B1-AS1ENST00000441672.1 linkuse as main transcriptn.97-24262A>G intron_variant, non_coding_transcript_variant 3
HSD11B1ENST00000261465.5 linkuse as main transcriptc.-49+1038T>C intron_variant 5
HSD11B1ENST00000367028.6 linkuse as main transcriptc.-49+1038T>C intron_variant 5 P1
HSD11B1ENST00000615289.4 linkuse as main transcriptc.-27+1038T>C intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.771
AC:
117232
AN:
151976
Hom.:
46510
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.587
Gnomad AMI
AF:
0.818
Gnomad AMR
AF:
0.786
Gnomad ASJ
AF:
0.893
Gnomad EAS
AF:
0.628
Gnomad SAS
AF:
0.703
Gnomad FIN
AF:
0.915
Gnomad MID
AF:
0.826
Gnomad NFE
AF:
0.865
Gnomad OTH
AF:
0.810
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.771
AC:
117296
AN:
152094
Hom.:
46530
Cov.:
32
AF XY:
0.773
AC XY:
57486
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.587
Gnomad4 AMR
AF:
0.786
Gnomad4 ASJ
AF:
0.893
Gnomad4 EAS
AF:
0.629
Gnomad4 SAS
AF:
0.703
Gnomad4 FIN
AF:
0.915
Gnomad4 NFE
AF:
0.865
Gnomad4 OTH
AF:
0.811
Alfa
AF:
0.837
Hom.:
34024
Bravo
AF:
0.758
Asia WGS
AF:
0.684
AC:
2377
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
10
DANN
Benign
0.72

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2235543; hg19: chr1-209860668; API