17-42555426-A-C

Variant names:

• chr17-42555426-A-C
• rs592389
• ENST00000585572.1:n.380-6193A>C

Variant summary

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

The ENST00000585572.1(ENSG00000266929):​n.380-6193A>C 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 151,998 control chromosomes in the GnomAD database, including 25,524 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 (25524 hom., cov: 32)
• Consequence: ENSG00000266929 ENST00000585572.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 18 publications found

Genes affected

ENSG00000266929 (HGNC:):

HSD17B1 (HGNC:5210): (hydroxysteroid 17-beta dehydrogenase 1) This gene encodes a member of the 17beta-hydroxysteroid dehydrogenase family of short-chain dehydrogenases/reductases. It has a dual function in estrogen activation and androgen inactivation and plays a major role in establishing the estrogen E2 concentration gradient between serum and peripheral tissues. The encoded protein catalyzes the last step in estrogen activation, using NADPH to convert estrogens E1 and E2 and androgens like 4-androstenedione, to testosterone. It has an N-terminal short-chain dehydrogenase domain with a cofactor binding site, and a narrow, hydrophobic C-terminal domain with a steroid substrate binding site. This gene is expressed primarily in the placenta and ovarian granulosa cells, and to a lesser extent, in the endometrium, adipose tissue, and prostate. Polymorphisms in this gene have been linked to breast and prostate cancer. A pseudogene of this gene has been identified. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585572.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B1	NM_000413.4	MANE Select	c.*488A>C		downstream_gene	N/A	NP_000404.2	P14061
	HSD17B1	NM_001330219.3		c.*488A>C		downstream_gene	N/A	NP_001317148.1	A0A0A0MQS7
	HSD17B1	NR_144397.2		n.*212A>C		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266929	ENST00000585572.1	TSL:4	n.380-6193A>C		intron	N/A
	HSD17B1	ENST00000585807.6	TSL:1 MANE Select	c.*488A>C		downstream_gene	N/A	ENSP00000466799.1	P14061
	HSD17B1	ENST00000225929.5	TSL:2	c.*488A>C		downstream_gene	N/A	ENSP00000225929.5	A0A0A0MQS7

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87227 AN: 151880 Hom.: 25494 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.574 AC: 87313 AN: 151998 Hom.: 25524 Cov.: 32 AF XY: 0.570 AC XY: 42352 AN XY: 74274

African (AFR) AF: 0.683 AC: 28317 AN: 41474

American (AMR) AF: 0.502 AC: 7675 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1355 AN: 3466

East Asian (EAS) AF: 0.439 AC: 2269 AN: 5168

South Asian (SAS) AF: 0.640 AC: 3079 AN: 4814

European-Finnish (FIN) AF: 0.530 AC: 5589 AN: 10546

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37370 AN: 67930

Other (OTH) AF: 0.526 AC: 1110 AN: 2112

Alfa AF: 0.562 Hom.: 9795

Bravo AF: 0.574

Asia WGS AF: 0.598 AC: 2083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.64
DANN	Benign	0.51
PhyloP100		-0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs592389; hg19: chr17-40707444;