GeneBe

9-96301920-CA-C

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_000197.2(HSD17B3):​c.154+30delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000619 in 1,452,792 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 19)
Exomes 𝑓: 0.0000062 ( 0 hom. )

Consequence

HSD17B3
NM_000197.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.71

Publications

2 publications found
Variant links:
Genes affected
HSD17B3 (HGNC:5212): (hydroxysteroid 17-beta dehydrogenase 3) This isoform of 17 beta-hydroxysteroid dehydrogenase is expressed predominantly in the testis and catalyzes the conversion of androstenedione to testosterone. It preferentially uses NADP as cofactor. Deficiency can result in male pseudohermaphroditism with gynecomastia. [provided by RefSeq, Jul 2008]
HSD17B3 Gene-Disease associations (from GenCC):
  • 46,XY disorder of sex development due to 17-beta-hydroxysteroid dehydrogenase 3 deficiency
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HSD17B3NM_000197.2 linkc.154+30delT intron_variant Intron 1 of 10 ENST00000375263.8 NP_000188.1
SLC35D2-HSD17B3NR_182427.1 linkn.2921+30delT intron_variant Intron 16 of 25

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HSD17B3ENST00000375263.8 linkc.154+30delT intron_variant Intron 1 of 10 1 NM_000197.2 ENSP00000364412.3
ENSG00000285269ENST00000643789.1 linkn.*1830+30delT intron_variant Intron 12 of 21 ENSP00000494818.1

Frequencies

GnomAD3 genomes
Cov.:
19
GnomAD4 exome
AF:
0.00000619
AC:
9
AN:
1452792
Hom.:
0
Cov.:
31
AF XY:
0.00000415
AC XY:
3
AN XY:
723386
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33422
American (AMR)
AF:
0.00
AC:
0
AN:
44712
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26066
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39660
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86152
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53324
Middle Eastern (MID)
AF:
0.000174
AC:
1
AN:
5750
European-Non Finnish (NFE)
AF:
0.00000725
AC:
8
AN:
1103606
Other (OTH)
AF:
0.00
AC:
0
AN:
60100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
19
Alfa
AF:
0.00
Hom.:
1826
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.7

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

Other links and lift over

dbSNP: rs8190483; hg19: chr9-99064202; COSMIC: COSV100931259; API