12-56769532-C-T

Variant names:

• chr12-56769532-C-T
• rs898611
• NM_003725.4:c.-19-4302C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003725.4(HSD17B6):​c.-19-4302C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,968 control chromosomes in the GnomAD database, including 26,337 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 0.57 (26337 hom., cov: 32)
• Consequence: HSD17B6 NM_003725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 19 publications found

Genes affected

HSD17B6 (HGNC:23316): (hydroxysteroid 17-beta dehydrogenase 6) The protein encoded by this gene has both oxidoreductase and epimerase activities and is involved in androgen catabolism. The oxidoreductase activity can convert 3 alpha-adiol to dihydrotestosterone, while the epimerase activity can convert androsterone to epi-androsterone. Both reactions use NAD+ as the preferred cofactor. This gene is a member of the retinol dehydrogenase family. [provided by RefSeq, Aug 2013]

ENSG00000309589 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD17B6	NM_003725.4	c.-19-4302C>T		intron_variant	Intron 1 of 4	ENST00000322165.1	NP_003716.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD17B6	ENST00000322165.1	c.-19-4302C>T		intron_variant	Intron 1 of 4	1	NM_003725.4	ENSP00000318631.1

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87278 AN: 151850 Hom.: 26334 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.574 AC: 87301 AN: 151968 Hom.: 26337 Cov.: 32 AF XY: 0.582 AC XY: 43197 AN XY: 74276

African (AFR) AF: 0.381 AC: 15779 AN: 41420

American (AMR) AF: 0.663 AC: 10121 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2010 AN: 3468

East Asian (EAS) AF: 0.730 AC: 3775 AN: 5170

South Asian (SAS) AF: 0.742 AC: 3568 AN: 4806

European-Finnish (FIN) AF: 0.698 AC: 7377 AN: 10562

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.626 AC: 42541 AN: 67970

Other (OTH) AF: 0.605 AC: 1276 AN: 2108

Alfa AF: 0.605 Hom.: 35566

Bravo AF: 0.561

Asia WGS AF: 0.730 AC: 2531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.33
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs898611; hg19: chr12-57163316; COSMIC: COSV59107872;