chr11-43856384-C-A

Variant names:

• chr11-43856384-C-A
• rs1061810
• NM_016142.3:c.*1136C>A

Variant summary

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

The NM_016142.3(HSD17B12):​c.*1136C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,842 control chromosomes in the GnomAD database, including 8,923 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 0.34 (8923 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: HSD17B12 NM_016142.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.852
• Publications: 59 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]

ENSG00000283375 (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 (AMR) allele frequency at 95% confidence interval = 0.418 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B12	NM_016142.3	MANE Select	c.*1136C>A		3_prime_UTR	Exon 11 of 11	NP_057226.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B12	ENST00000278353.10	TSL:1 MANE Select	c.*1136C>A		3_prime_UTR	Exon 11 of 11	ENSP00000278353.4
	HSD17B12	ENST00000525736.1	TSL:1	n.4059C>A		non_coding_transcript_exon	Exon 2 of 2
	HSD17B12	ENST00000865203.1		c.*1136C>A		3_prime_UTR	Exon 12 of 12	ENSP00000535262.1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50861 AN: 151726 Hom.: 8902 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.336

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.335 AC: 50917 AN: 151842 Hom.: 8923 Cov.: 31 AF XY: 0.335 AC XY: 24867 AN XY: 74174

African (AFR) AF: 0.400 AC: 16550 AN: 41404

American (AMR) AF: 0.426 AC: 6500 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3466

East Asian (EAS) AF: 0.243 AC: 1255 AN: 5156

South Asian (SAS) AF: 0.321 AC: 1540 AN: 4804

European-Finnish (FIN) AF: 0.310 AC: 3263 AN: 10524

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19550 AN: 67922

Other (OTH) AF: 0.334 AC: 705 AN: 2110

Alfa AF: 0.308 Hom.: 14835

Bravo AF: 0.349

Asia WGS AF: 0.311 AC: 1079 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.9
DANN	Benign	0.60
PhyloP100		0.85
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: rs1061810; hg19: chr11-43877934;