chr11-43686859-G-A

Position:

• chr11-43686859-G-A

Variant summary

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

The NM_016142.3(HSD17B12):​c.160+5872G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,964 control chromosomes in the GnomAD database, including 19,516 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 0.50 (19516 hom., cov: 31)
• Consequence: HSD17B12 NM_016142.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD17B12	NM_016142.3	c.160+5872G>A		intron_variant		ENST00000278353.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B12	ENST00000278353.10	c.160+5872G>A		intron_variant		1	NM_016142.3	P1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76080 AN: 151846 Hom.: 19488 Cov.: 31

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.501 AC: 76153 AN: 151964 Hom.: 19516 Cov.: 31 AF XY: 0.495 AC XY: 36742 AN XY: 74258

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.495

Alfa AF: 0.509 Hom.: 2457

Bravo AF: 0.494

Asia WGS AF: 0.377 AC: 1314 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.1
DANN	Benign	0.45

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: rs10838151; hg19: chr11-43708409;