11-43781704-G-A

Variant names:

• chr11-43781704-G-A
• rs4755741
• NM_016142.3:c.284-16616G>A

Variant summary

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

The NM_016142.3(HSD17B12):​c.284-16616G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,910 control chromosomes in the GnomAD database, including 33,053 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 0.66 (33053 hom., cov: 31)
• Consequence: HSD17B12 NM_016142.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 12 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016142.3. 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
	HSD17B12	NM_016142.3	MANE Select	c.284-16616G>A		intron	N/A	NP_057226.1	Q53GQ0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B12	ENST00000278353.10	TSL:1 MANE Select	c.284-16616G>A		intron	N/A	ENSP00000278353.4	Q53GQ0-1
	HSD17B12	ENST00000865203.1		c.284-16616G>A		intron	N/A	ENSP00000535262.1
	HSD17B12	ENST00000865204.1		c.284-16619G>A		intron	N/A	ENSP00000535263.1

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99642 AN: 151794 Hom.: 33008 Cov.: 31

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.657 AC: 99729 AN: 151910 Hom.: 33053 Cov.: 31 AF XY: 0.657 AC XY: 48778 AN XY: 74236

African (AFR) AF: 0.601 AC: 24881 AN: 41368

American (AMR) AF: 0.561 AC: 8550 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2182 AN: 3472

East Asian (EAS) AF: 0.747 AC: 3861 AN: 5172

South Asian (SAS) AF: 0.676 AC: 3263 AN: 4824

European-Finnish (FIN) AF: 0.682 AC: 7186 AN: 10540

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47545 AN: 67992

Other (OTH) AF: 0.660 AC: 1390 AN: 2106

Alfa AF: 0.682 Hom.: 34841

Bravo AF: 0.643

Asia WGS AF: 0.694 AC: 2399 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.48
PhyloP100		-1.2
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: rs4755741; hg19: chr11-43803254;