rs6564961

chr16-82045486-G-A

Variant summary

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

The NM_002153.3(HSD17B2):c.265+9797G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 152,102 control chromosomes in the GnomAD database, including 27,858 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 0.60 (27858 hom., cov: 33)
• Consequence: HSD17B2 NM_002153.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD17B2	NM_002153.3	c.265+9797G>A		intron_variant		ENST00000199936.9
HSD17B2-AS1	XR_933797.3	n.3675-878C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B2	ENST00000199936.9	c.265+9797G>A		intron_variant		1	NM_002153.3	P1
HSD17B2-AS1	ENST00000567021.1	n.592-878C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91527 AN: 151984 Hom.: 27820 Cov.: 33

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.602 AC: 91623 AN: 152102 Hom.: 27858 Cov.: 33 AF XY: 0.600 AC XY: 44615 AN XY: 74366

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.579

Alfa AF: 0.604 Hom.: 26983

Bravo AF: 0.608

Asia WGS AF: 0.455 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	5.4
Dann	Benign	0.66

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: rs6564961; hg19: chr16-82079091;