rs6564961

Variant names:

• chr16-82045486-G-A
• rs6564961
• NM_002153.3:c.265+9797G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HSD17B2	NM_002153.3	c.265+9797G>A		intron_variant	Intron 1 of 4	ENST00000199936.9	NP_002144.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD17B2	ENST00000199936.9	c.265+9797G>A		intron_variant	Intron 1 of 4	1	NM_002153.3	ENSP00000199936.4

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

African (AFR) AF: 0.634 AC: 26286 AN: 41476

American (AMR) AF: 0.656 AC: 10030 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1683 AN: 3468

East Asian (EAS) AF: 0.329 AC: 1700 AN: 5170

South Asian (SAS) AF: 0.516 AC: 2489 AN: 4820

European-Finnish (FIN) AF: 0.587 AC: 6214 AN: 10580

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41338 AN: 67986

Other (OTH) AF: 0.579 AC: 1221 AN: 2110

Alfa AF: 0.606 Hom.: 35698

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
PhyloP100		0.53
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6564961; hg19: chr16-82079091;