rs10838149

chr11-43684073-C-Gchr11-43684073-C-T

Variant summary

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

The NM_016142.3(HSD17B12):c.160+3086C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,038 control chromosomes in the GnomAD database, including 18,999 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 (18999 hom., cov: 33)
• Consequence: HSD17B12 NM_016142.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD17B12	NM_016142.3	c.160+3086C>G		intron_variant		ENST00000278353.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B12	ENST00000278353.10	c.160+3086C>G		intron_variant		1	NM_016142.3	P1

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75104 AN: 151920 Hom.: 18979 Cov.: 33

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.494 AC: 75163 AN: 152038 Hom.: 18999 Cov.: 33 AF XY: 0.488 AC XY: 36306 AN XY: 74324

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.494

Alfa AF: 0.504 Hom.: 2418

Bravo AF: 0.486

Asia WGS AF: 0.374 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.1
Dann	Benign	0.18

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: rs10838149; hg19: chr11-43705623; COSMIC: COSV53496475;