rs1061810

chr11-43856384-C-A

Variant summary

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

The NM_016142.3(HSD17B12):c.*1136C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,842 control chromosomes in the GnomAD database, including 8,923 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 0.34 (8923 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: HSD17B12 NM_016142.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.852

Genes affected

HSD17B12 (HGNC:18646): (hydroxysteroid 17-beta dehydrogenase 12) This gene encodes a very important 17beta-hydroxysteroid dehydrogenase (17beta-HSD) that converts estrone into estradiol in ovarian tissue. This enzyme is also involved in fatty acid elongation. [provided by RefSeq, Oct 2011]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD17B12	NM_016142.3	c.*1136C>A		3_prime_UTR_variant	11/11	ENST00000278353.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B12	ENST00000278353.10	c.*1136C>A		3_prime_UTR_variant	11/11	1	NM_016142.3	P1
	ENST00000637427.1	n.21G>T		non_coding_transcript_exon_variant	1/2	5
	ENST00000530450.1	n.248-7868G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50861 AN: 151726 Hom.: 8902 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.336

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.335 AC: 50917 AN: 151842 Hom.: 8923 Cov.: 31 AF XY: 0.335 AC XY: 24867 AN XY: 74174

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.334

Alfa AF: 0.306 Hom.: 3290

Bravo AF: 0.349

Asia WGS AF: 0.311 AC: 1079 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	5.9
Dann	Benign	0.60

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: rs1061810; hg19: chr11-43877934;