16-82097973-C-G

Variant summary

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

The NM_002153.3(HSD17B2):c.803-102C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 1,057,096 control chromosomes in the GnomAD database, including 442,650 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 0.84 (54747 hom., cov: 30)
  • Exomes 𝑓: 0.92 (387903 hom.)
• Consequence: HSD17B2 NM_002153.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

Genes affected

HSD17B2 (HGNC:5211): (hydroxysteroid 17-beta dehydrogenase 2) Enables estradiol 17-beta-dehydrogenase activity and testosterone dehydrogenase (NAD+) activity. Involved in response to retinoic acid. Predicted to be located in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

HSD17B2-AS1 (HGNC:56281): (HSD17B2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD17B2	NM_002153.3	c.803-102C>G		intron_variant		ENST00000199936.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B2	ENST00000199936.9	c.803-102C>G		intron_variant		1	NM_002153.3	P1
HSD17B2-AS1	ENST00000567021.1	n.44-26784G>C		intron_variant, non_coding_transcript_variant		5
HSD17B2	ENST00000566838.2	c.*6797C>G		3_prime_UTR_variant	3/3	2
HSD17B2	ENST00000568090.5	c.395-102C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127126 AN: 151582 Hom.: 54723 Cov.: 30

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.867

GnomAD4 exome AF: 0.921 AC: 834191 AN: 905396 Hom.: 387903 Cov.: 12 AF XY: 0.922 AC XY: 418873 AN XY: 454524

Gnomad4 AFR exome AF: 0.644

Gnomad4 AMR exome AF: 0.657

Gnomad4 ASJ exome AF: 0.941

Gnomad4 EAS exome AF: 0.655

Gnomad4 SAS exome AF: 0.862

Gnomad4 FIN exome AF: 0.931

Gnomad4 NFE exome AF: 0.955

Gnomad4 OTH exome AF: 0.902

GnomAD4 genome AF: 0.838 AC: 127193 AN: 151700 Hom.: 54747 Cov.: 30 AF XY: 0.834 AC XY: 61842 AN XY: 74124

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.950

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.953

Gnomad4 OTH AF: 0.865

Alfa AF: 0.873 Hom.: 3044

Bravo AF: 0.816

Asia WGS AF: 0.760 AC: 2638 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.12
Dann	Benign	0.36

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: rs2955160; hg19: chr16-82131578;