rs7201637

Positions:

• chr16-82081670-T-A

Variant summary

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

The NM_002153.3(HSD17B2):​c.665-9232T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0908 in 152,306 control chromosomes in the GnomAD database, including 1,120 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 0.091 (1120 hom., cov: 32)
• Consequence: HSD17B2 NM_002153.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSD17B2	NM_002153.3	c.665-9232T>A		intron_variant		ENST00000199936.9	NP_002144.1
HSD17B2	XM_047434049.1	c.665-8495T>A		intron_variant			XP_047290005.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSD17B2	ENST00000199936.9	c.665-9232T>A		intron_variant		1	NM_002153.3	ENSP00000199936.4
HSD17B2	ENST00000568090.5	c.257-9232T>A		intron_variant		3		ENSP00000456529.1
HSD17B2	ENST00000566838.2	c.293-9232T>A		intron_variant		2		ENSP00000456471.1
HSD17B2-AS1	ENST00000567021.1	n.44-10481A>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0907 AC: 13806 AN: 152188 Hom.: 1114 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0542

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0367

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.0908 AC: 13831 AN: 152306 Hom.: 1120 Cov.: 32 AF XY: 0.0926 AC XY: 6896 AN XY: 74490

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.0537

Gnomad4 FIN AF: 0.0240

Gnomad4 NFE AF: 0.0366

Gnomad4 OTH AF: 0.0907

Alfa AF: 0.0675 Hom.: 71

Bravo AF: 0.109

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.30

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: rs7201637; hg19: chr16-82115275;