16-82094817-T-C

Position:

• chr16-82094817-T-C

Variant summary

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

The ENST00000199936.9(HSD17B2):​c.803-3258T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,982 control chromosomes in the GnomAD database, including 24,603 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 0.57 (24603 hom., cov: 31)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: HSD17B2 ENST00000199936.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSD17B2	NM_002153.3	c.803-3258T>C		intron_variant		ENST00000199936.9	NP_002144.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSD17B2	ENST00000199936.9	c.803-3258T>C		intron_variant		1	NM_002153.3	ENSP00000199936	P1
HSD17B2-AS1	ENST00000567021.1	n.44-23628A>G		intron_variant, non_coding_transcript_variant		5
HSD17B2	ENST00000566838.2	c.*3641T>C		3_prime_UTR_variant	3/3	2		ENSP00000456471
HSD17B2	ENST00000568090.5	c.395-3258T>C		intron_variant		3		ENSP00000456529

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85980 AN: 151860 Hom.: 24593 Cov.: 31

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.593

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.566 AC: 86010 AN: 151978 Hom.: 24603 Cov.: 31 AF XY: 0.561 AC XY: 41643 AN XY: 74276

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.587

Alfa AF: 0.607 Hom.: 50821

Bravo AF: 0.561

Asia WGS AF: 0.470 AC: 1633 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.80

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: rs4888202; hg19: chr16-82128422;