rs1424151

chr16-82095747-A-G

Variant summary

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

The NM_002153.3(HSD17B2):c.803-2328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0761 in 152,316 control chromosomes in the GnomAD database, including 822 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 0.076 (822 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HSD17B2 NM_002153.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD17B2	NM_002153.3	c.803-2328A>G		intron_variant		ENST00000199936.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B2	ENST00000199936.9	c.803-2328A>G		intron_variant		1	NM_002153.3	P1
HSD17B2-AS1	ENST00000567021.1	n.44-24558T>C		intron_variant, non_coding_transcript_variant		5
HSD17B2	ENST00000566838.2	c.*4571A>G		3_prime_UTR_variant	3/3	2
HSD17B2	ENST00000568090.5	c.395-2328A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 11556 AN: 152198 Hom.: 815 Cov.: 33

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.0666

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0367

Gnomad OTH AF: 0.0783

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0761 AC: 11586 AN: 152316 Hom.: 822 Cov.: 33 AF XY: 0.0787 AC XY: 5861 AN XY: 74496

Gnomad4 AFR AF: 0.0909

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.0663

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0366

Gnomad4 OTH AF: 0.0794

Alfa AF: 0.0545 Hom.: 260

Bravo AF: 0.0928

Asia WGS AF: 0.118 AC: 408 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.15
Dann	Benign	0.60

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: rs1424151; hg19: chr16-82129352;