rs2955163

Variant names:

• chr16-82094592-C-G
• rs2955163
• NM_002153.3:c.803-3483C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-82094592-C-G
• chr16-82094592-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002153.3(HSD17B2):​c.803-3483C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 152,166 control chromosomes in the GnomAD database, including 60,111 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 0.88 (60108 hom., cov: 31)
  • Exomes 𝑓: 1.0 (3 hom.)
• Consequence: HSD17B2 NM_002153.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD17B2	NM_002153.3	c.803-3483C>G		intron_variant	Intron 4 of 4	ENST00000199936.9	NP_002144.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD17B2	ENST00000199936.9	c.803-3483C>G		intron_variant	Intron 4 of 4	1	NM_002153.3	ENSP00000199936.4
HSD17B2	ENST00000566838.2	c.*3416C>G		3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000456471.1
HSD17B2	ENST00000568090.5	c.395-3483C>G		intron_variant	Intron 4 of 4	3		ENSP00000456529.1
HSD17B2-AS1	ENST00000567021.2	n.44-23403G>C		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134381 AN: 152042 Hom.: 60074 Cov.: 31

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.889

GnomAD4 exome AF: 1.00 AC: 6 AN: 6 Hom.: 3 Cov.: 0 AF XY: 1.00 AC XY: 4 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 6 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.884 AC: 134463 AN: 152160 Hom.: 60108 Cov.: 31 AF XY: 0.878 AC XY: 65290 AN XY: 74382

African (AFR) AF: 0.837 AC: 34722 AN: 41480

American (AMR) AF: 0.758 AC: 11580 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3336 AN: 3472

East Asian (EAS) AF: 0.618 AC: 3194 AN: 5166

South Asian (SAS) AF: 0.796 AC: 3836 AN: 4822

European-Finnish (FIN) AF: 0.938 AC: 9955 AN: 10610

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.953 AC: 64817 AN: 68024

Other (OTH) AF: 0.885 AC: 1864 AN: 2106

Alfa AF: 0.916 Hom.: 7570

Bravo AF: 0.870

Asia WGS AF: 0.691 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.39
PhyloP100		-0.54
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: rs2955163; hg19: chr16-82128197;