rs13302476

chr9-96272904-T-Achr9-96272904-T-Cchr9-96272904-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000197.2(HSD17B3):c.202-17961A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,034 control chromosomes in the GnomAD database, including 3,602 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 0.20 (3602 hom., cov: 31)
• Consequence: HSD17B3 NM_000197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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]

SLC35D2-HSD17B3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD17B3	NM_000197.2	c.202-17961A>T		intron_variant		ENST00000375263.8
SLC35D2-HSD17B3	NR_182427.1	n.2969-17961A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B3	ENST00000375263.8	c.202-17961A>T		intron_variant		1	NM_000197.2	P1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30148 AN: 151916 Hom.: 3601 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.199 AC: 30196 AN: 152034 Hom.: 3602 Cov.: 31 AF XY: 0.203 AC XY: 15118 AN XY: 74342

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.215

Alfa AF: 0.0672 Hom.: 70

Bravo AF: 0.206

Asia WGS AF: 0.394 AC: 1371 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	0.22
Dann	Benign	0.37

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

Other links and lift over

dbSNP: rs13302476; hg19: chr9-99035186;