Variant chr1-209706871-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_005525.4(HSD11B1):c.331+53dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 1,607,542 control chromosomes in the GnomAD database, including 32,985 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.20 ( 2975 hom., cov: 27)

Exomes 𝑓: 0.20 ( 30010 hom. )

Consequence

HSD11B1
NM_005525.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.117

Variant links:

Genes affected

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]

HSD11B1 links:

HSD11B1-AS1 (HGNC:54053): (HSD11B1 antisense RNA 1)

HSD11B1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-209706871-C-CA is Benign according to our data. Variant chr1-209706871-C-CA is described in ClinVar as [Benign]. Clinvar id is 375731.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD11B1	NM_005525.4 linkuse as main transcript	c.331+53dup		intron_variant		ENST00000367027.5
HSD11B1-AS1	NR_134510.1 linkuse as main transcript	n.66+35625_66+35626insT		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD11B1	ENST00000367027.5 linkuse as main transcript	c.331+53dup		intron_variant		1	NM_005525.4	P1
HSD11B1-AS1	ENST00000441672.1 linkuse as main transcript	n.96+17158_96+17159insT		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

29822

AN:

152020

Hom.:

2965

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.210

Gnomad EAS

AF:

0.217

Gnomad SAS

AF:

0.170

Gnomad FIN

AF:

0.263

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.188

GnomAD3 exomes

AF:

0.207

AC:

51922

AN:

250970

Hom.:

5608

AF XY:

0.205

AC XY:

27794

AN XY:

135614

show subpopulations

Gnomad AFR exome

AF:

0.179

Gnomad AMR exome

AF:

0.209

Gnomad ASJ exome

AF:

0.212

Gnomad EAS exome

AF:

0.230

Gnomad SAS exome

AF:

0.175

Gnomad FIN exome

AF:

0.264

Gnomad NFE exome

AF:

0.204

Gnomad OTH exome

AF:

0.199

GnomAD4 exome

AF:

0.200

AC:

291594

AN:

1455404

Hom.:

30010

Cov.:

AF XY:

0.199

AC XY:

144282

AN XY:

724400

show subpopulations

Gnomad4 AFR exome

AF:

0.175

Gnomad4 AMR exome

AF:

0.208

Gnomad4 ASJ exome

AF:

0.211

Gnomad4 EAS exome

AF:

0.183

Gnomad4 SAS exome

AF:

0.176

Gnomad4 FIN exome

AF:

0.263

Gnomad4 NFE exome

AF:

0.200

Gnomad4 OTH exome

AF:

0.206

GnomAD4 genome

AF:

0.196

AC:

29863

AN:

152138

Hom.:

2975

Cov.:

AF XY:

0.197

AC XY:

14654

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.179

Gnomad4 AMR

AF:

0.176

Gnomad4 ASJ

AF:

0.210

Gnomad4 EAS

AF:

0.216

Gnomad4 SAS

AF:

0.170

Gnomad4 FIN

AF:

0.263

Gnomad4 NFE

AF:

0.201

Gnomad4 OTH

AF:

0.190

Alfa

AF:

0.205

Hom.:

598

Bravo

AF:

0.193

Asia WGS

AF:

0.211

AC:

734

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Cortisone reductase deficiency 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Mendelics

Jan 23, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over