dbSNP rs4545339: HSD11B1-AS1:n.169-15253G>C (chr1-209739397-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000441672.2(HSD11B1-AS1):n.169-15253G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.052 in 152,144 control chromosomes in the GnomAD database, including 637 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 0.052 ( 637 hom., cov: 32)

Consequence

HSD11B1-AS1
ENST00000441672.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00600

Publications

3 publications found

Variant links:

Genes affected

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

HSD11B1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD11B1-AS1	NR_134510.1 link	n.66+3100G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HSD11B1-AS1	ENST00000441672.2 link	n.169-15253G>C	intron_variant	Intron 1 of 3	3
HSD11B1-AS1	ENST00000774900.1 link	n.121+18079G>C	intron_variant	Intron 1 of 2
HSD11B1-AS1	ENST00000774901.1 link	n.141+3100G>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0521

AC:

7917

AN:

152026

Hom.:

634

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0474

Gnomad AMI

AF:

0.0308

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.300

Gnomad SAS

AF:

0.0990

Gnomad FIN

AF:

0.0124

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.0123

Gnomad OTH

AF:

0.0421

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0520

AC:

7916

AN:

152144

Hom.:

637

Cov.:

AF XY:

0.0574

AC XY:

4269

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.0472

AC:

1960

AN:

41518

American (AMR)

AF:

0.184

AC:

2807

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

AN:

3468

East Asian (EAS)

AF:

0.300

AC:

1538

AN:

5130

South Asian (SAS)

AF:

0.0985

AC:

474

AN:

4814

European-Finnish (FIN)

AF:

0.0124

AC:

131

AN:

10590

Middle Eastern (MID)

AF:

0.00342

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0123

AC:

837

AN:

68018

Other (OTH)

AF:

0.0416

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

328

655

983

1310

1638

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

252

336

420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00356

Hom.:

Bravo

AF:

0.0648

Asia WGS

AF:

0.160

AC:

555

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.8

(source)

DANN

Benign

0.66

PhyloP100

-0.0060

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over