rs10838162

Variant names:

• chr11-43767672-A-G
• rs10838162
• NM_016142.3:c.283+13551A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-43767672-A-G
• chr11-43767672-A-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.283+13551A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,012 control chromosomes in the GnomAD database, including 33,006 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 0.66 (33006 hom., cov: 32)
• Consequence: HSD17B12 NM_016142.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD17B12	NM_016142.3	c.283+13551A>G		intron_variant	Intron 3 of 10	ENST00000278353.10	NP_057226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD17B12	ENST00000278353.10	c.283+13551A>G		intron_variant	Intron 3 of 10	1	NM_016142.3	ENSP00000278353.4

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99581 AN: 151894 Hom.: 32964 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.724

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.656 AC: 99663 AN: 152012 Hom.: 33006 Cov.: 32 AF XY: 0.657 AC XY: 48772 AN XY: 74282

African (AFR) AF: 0.598 AC: 24801 AN: 41454

American (AMR) AF: 0.561 AC: 8560 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2182 AN: 3472

East Asian (EAS) AF: 0.746 AC: 3862 AN: 5174

South Asian (SAS) AF: 0.677 AC: 3265 AN: 4822

European-Finnish (FIN) AF: 0.683 AC: 7196 AN: 10540

Middle Eastern (MID) AF: 0.721 AC: 209 AN: 290

European-Non Finnish (NFE) AF: 0.699 AC: 47529 AN: 67968

Other (OTH) AF: 0.660 AC: 1397 AN: 2116

Alfa AF: 0.678 Hom.: 4590

Bravo AF: 0.642

Asia WGS AF: 0.693 AC: 2394 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.81
PhyloP100		-0.058
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: rs10838162; hg19: chr11-43789222;