11-43742137-A-T

Variant names:

• chr11-43742137-A-T
• rs2862993
• NM_016142.3:c.161-8774A>T

Variant summary

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

The NM_016142.3(HSD17B12):​c.161-8774A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.22 (1417 hom., cov: 16)
• Consequence: HSD17B12 NM_016142.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B12	NM_016142.3	MANE Select	c.161-8774A>T		intron	N/A	NP_057226.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B12	ENST00000278353.10	TSL:1 MANE Select	c.161-8774A>T		intron	N/A	ENSP00000278353.4
	HSD17B12	ENST00000395700.4	TSL:1	c.161-8774A>T		intron	N/A	ENSP00000379052.4
	HSD17B12	ENST00000637401.1	TSL:4	c.161-8774A>T		intron	N/A	ENSP00000490421.1

Frequencies

GnomAD3 genomes AF: 0.218 AC: 18510 AN: 84848 Hom.: 1417 Cov.: 16

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.218 AC: 18511 AN: 84830 Hom.: 1417 Cov.: 16 AF XY: 0.215 AC XY: 8743 AN XY: 40596

African (AFR) AF: 0.297 AC: 5998 AN: 20226

American (AMR) AF: 0.157 AC: 1399 AN: 8938

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 413 AN: 1910

East Asian (EAS) AF: 0.151 AC: 532 AN: 3516

South Asian (SAS) AF: 0.227 AC: 536 AN: 2366

European-Finnish (FIN) AF: 0.176 AC: 758 AN: 4316

Middle Eastern (MID) AF: 0.227 AC: 29 AN: 128

European-Non Finnish (NFE) AF: 0.204 AC: 8552 AN: 41882

Other (OTH) AF: 0.220 AC: 238 AN: 1084

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.98
DANN	Benign	0.18
PhyloP100		0.11
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: rs2862993; hg19: chr11-43763687;