9-96287419-T-C

Variant summary

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

The NM_000197.2(HSD17B3):​c.201+10997A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,082 control chromosomes in the GnomAD database, including 12,341 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 0.39 ( 12341 hom., cov: 33)

Consequence

HSD17B3
NM_000197.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.492
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HSD17B3NM_000197.2 linkuse as main transcriptc.201+10997A>G intron_variant ENST00000375263.8
SLC35D2-HSD17B3NR_182427.1 linkuse as main transcriptn.2968+10997A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HSD17B3ENST00000375263.8 linkuse as main transcriptc.201+10997A>G intron_variant 1 NM_000197.2 P1P37058-1

Frequencies

GnomAD3 genomes
AF:
0.395
AC:
59958
AN:
151964
Hom.:
12343
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.496
Gnomad AMI
AF:
0.315
Gnomad AMR
AF:
0.300
Gnomad ASJ
AF:
0.413
Gnomad EAS
AF:
0.264
Gnomad SAS
AF:
0.287
Gnomad FIN
AF:
0.356
Gnomad MID
AF:
0.472
Gnomad NFE
AF:
0.378
Gnomad OTH
AF:
0.389
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.394
AC:
59992
AN:
152082
Hom.:
12341
Cov.:
33
AF XY:
0.389
AC XY:
28911
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.495
Gnomad4 AMR
AF:
0.300
Gnomad4 ASJ
AF:
0.413
Gnomad4 EAS
AF:
0.264
Gnomad4 SAS
AF:
0.289
Gnomad4 FIN
AF:
0.356
Gnomad4 NFE
AF:
0.378
Gnomad4 OTH
AF:
0.392
Alfa
AF:
0.372
Hom.:
1872
Bravo
AF:
0.397
Asia WGS
AF:
0.268
AC:
933
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.89
DANN
Benign
0.58

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.

Other links and lift over

dbSNP: rs280663; hg19: chr9-99049701; API