GeneBe

rs4393158

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000441672.2(HSD11B1-AS1):​n.284-15491T>G variant causes a intron 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
ENST00000441672.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.376

Publications

8 publications found
Variant links:
Genes affected
HSD11B1-AS1 (HGNC:54053): (HSD11B1 antisense RNA 1)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HSD11B1-AS1NR_134509.1 linkn.97-15491T>G intron_variant Intron 1 of 2
HSD11B1-AS1NR_134510.1 linkn.67-15491T>G intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HSD11B1-AS1ENST00000441672.2 linkn.284-15491T>G intron_variant Intron 2 of 3 3
HSD11B1-AS1ENST00000774900.1 linkn.122-15491T>G intron_variant Intron 1 of 2
HSD11B1-AS1ENST00000774901.1 linkn.142-15491T>G intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
31
Alfa
AF:
0.00
Hom.:
143926

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.2
DANN
Benign
0.48
PhyloP100
-0.38

Splicing

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

Publications

Other links and lift over

dbSNP: rs4393158; hg19: chr1-209851897; API