11-43721280-C-T

Variant names:

• chr11-43721280-C-T
• rs11037579
• NM_016142.3:c.161-29631C>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.161-29631C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,734 control chromosomes in the GnomAD database, including 19,025 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 0.49 (19025 hom., cov: 30)
• Consequence: HSD17B12 NM_016142.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD17B12	NM_016142.3	c.161-29631C>T		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.161-29631C>T		intron_variant	Intron 1 of 10	1	NM_016142.3	ENSP00000278353.4

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75045 AN: 151616 Hom.: 19008 Cov.: 30

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.495 AC: 75100 AN: 151734 Hom.: 19025 Cov.: 30 AF XY: 0.489 AC XY: 36246 AN XY: 74116

African (AFR) AF: 0.497 AC: 20559 AN: 41346

American (AMR) AF: 0.394 AC: 5991 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2145 AN: 3464

East Asian (EAS) AF: 0.227 AC: 1171 AN: 5158

South Asian (SAS) AF: 0.452 AC: 2167 AN: 4794

European-Finnish (FIN) AF: 0.518 AC: 5449 AN: 10528

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.528 AC: 35904 AN: 67938

Other (OTH) AF: 0.492 AC: 1035 AN: 2104

Alfa AF: 0.504 Hom.: 3286

Bravo AF: 0.487

Asia WGS AF: 0.381 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.6
DANN	Benign	0.75
PhyloP100		-0.11
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: rs11037579; hg19: chr11-43742830;