11-43697551-C-T

Position:

• chr11-43697551-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+16564C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,988 control chromosomes in the GnomAD database, including 7,536 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 0.31 (7536 hom., cov: 32)
• Consequence: HSD17B12 NM_016142.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSD17B12	NM_016142.3	c.160+16564C>T		intron_variant		ENST00000278353.10	NP_057226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSD17B12	ENST00000278353.10	c.160+16564C>T		intron_variant		1	NM_016142.3	ENSP00000278353.4

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47428 AN: 151870 Hom.: 7529 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.312 AC: 47439 AN: 151988 Hom.: 7536 Cov.: 32 AF XY: 0.309 AC XY: 22986 AN XY: 74298

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.315

Alfa AF: 0.303 Hom.: 1191

Bravo AF: 0.311

Asia WGS AF: 0.288 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.55
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs7928523; hg19: chr11-43719101;