11-43706780-T-C

Variant names:

• chr11-43706780-T-C
• rs11037575
• NM_016142.3:c.160+25793T>C

Variant summary

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

The NM_016142.3(HSD17B12):​c.160+25793T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 150,924 control chromosomes in the GnomAD database, including 11,714 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 0.37 (11714 hom., cov: 28)
• Consequence: HSD17B12 NM_016142.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 30 publications found

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]

ENSG00000283341 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD17B12	NM_016142.3	c.160+25793T>C		intron_variant	Intron 1 of 10	ENST00000278353.10	NP_057226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD17B12	ENST00000278353.10	c.160+25793T>C		intron_variant	Intron 1 of 10	1	NM_016142.3	ENSP00000278353.4

Frequencies

GnomAD3 genomes AF: 0.370 AC: 55805 AN: 150814 Hom.: 11702 Cov.: 28

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.370 AC: 55831 AN: 150924 Hom.: 11714 Cov.: 28 AF XY: 0.378 AC XY: 27822 AN XY: 73636

African (AFR) AF: 0.183 AC: 7513 AN: 41030

American (AMR) AF: 0.531 AC: 8048 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 881 AN: 3454

East Asian (EAS) AF: 0.718 AC: 3681 AN: 5130

South Asian (SAS) AF: 0.419 AC: 1991 AN: 4756

European-Finnish (FIN) AF: 0.445 AC: 4583 AN: 10296

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27892 AN: 67806

Other (OTH) AF: 0.390 AC: 815 AN: 2092

Alfa AF: 0.397 Hom.: 29722

Bravo AF: 0.368

Asia WGS AF: 0.529 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.55
PhyloP100		-0.097
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11037575; hg19: chr11-43728330;