1-119512152-A-G

Variant summary

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

The NM_000862.3(HSD3B1):​c.310+485A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,128 control chromosomes in the GnomAD database, including 46,852 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 0.78 ( 46852 hom., cov: 32)

Consequence

HSD3B1
NM_000862.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0620
Variant links:
Genes affected
HSD3B1 (HGNC:5217): (hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1) The protein encoded by this gene is an enzyme that catalyzes the oxidative conversion of delta-5-3-beta-hydroxysteroid precursors into delta-4-ketosteroids, which leads to the production of all classes of steroid hormones. The encoded protein also catalyzes the interconversion of 3-beta-hydroxy- and 3-keto-5-alpha-androstane steroids. [provided by RefSeq, Jun 2016]

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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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HSD3B1NM_000862.3 linkc.310+485A>G intron_variant Intron 3 of 3 ENST00000369413.8 NP_000853.1 P14060
HSD3B1NM_001328615.1 linkc.310+485A>G intron_variant Intron 3 of 3 NP_001315544.1 P14060

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HSD3B1ENST00000369413.8 linkc.310+485A>G intron_variant Intron 3 of 3 1 NM_000862.3 ENSP00000358421.3 P14060
HSD3B1ENST00000528909.1 linkc.310+485A>G intron_variant Intron 2 of 2 1 ENSP00000432268.1 P14060
HSD3B1ENST00000492140.1 linkn.*200A>G downstream_gene_variant 2

Frequencies

GnomAD3 genomes
AF:
0.780
AC:
118571
AN:
152010
Hom.:
46805
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.888
Gnomad AMI
AF:
0.841
Gnomad AMR
AF:
0.811
Gnomad ASJ
AF:
0.690
Gnomad EAS
AF:
0.923
Gnomad SAS
AF:
0.863
Gnomad FIN
AF:
0.750
Gnomad MID
AF:
0.737
Gnomad NFE
AF:
0.700
Gnomad OTH
AF:
0.753
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.780
AC:
118675
AN:
152128
Hom.:
46852
Cov.:
32
AF XY:
0.786
AC XY:
58481
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.888
Gnomad4 AMR
AF:
0.811
Gnomad4 ASJ
AF:
0.690
Gnomad4 EAS
AF:
0.923
Gnomad4 SAS
AF:
0.862
Gnomad4 FIN
AF:
0.750
Gnomad4 NFE
AF:
0.700
Gnomad4 OTH
AF:
0.756
Alfa
AF:
0.734
Hom.:
19987
Bravo
AF:
0.787
Asia WGS
AF:
0.877
AC:
3049
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
6.9
DANN
Benign
0.41

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: rs6428830; hg19: chr1-120054775; API