rs1364287

chr16-82085495-G-Achr16-82085495-G-T

Variant summary

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

The NM_002153.3(HSD17B2):c.665-5407G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,976 control chromosomes in the GnomAD database, including 6,611 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 0.28 (6611 hom., cov: 32)
• Consequence: HSD17B2 NM_002153.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD17B2	NM_002153.3	c.665-5407G>A		intron_variant		ENST00000199936.9
HSD17B2	XM_047434049.1	c.665-4670G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B2	ENST00000199936.9	c.665-5407G>A		intron_variant		1	NM_002153.3	P1
HSD17B2-AS1	ENST00000567021.1	n.44-14306C>T		intron_variant, non_coding_transcript_variant		5
HSD17B2	ENST00000566838.2	c.293-5407G>A		intron_variant		2
HSD17B2	ENST00000568090.5	c.257-5407G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42152 AN: 151858 Hom.: 6609 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.0601

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.277 AC: 42160 AN: 151976 Hom.: 6611 Cov.: 32 AF XY: 0.277 AC XY: 20593 AN XY: 74252

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.0599

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.273

Alfa AF: 0.320 Hom.: 8647

Bravo AF: 0.260

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.0030
Dann	Benign	0.40

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: rs1364287; hg19: chr16-82119100;