dbSNP rs8191246: HSD17B2:p.Ter388Trpext*? (chr16-82098435-A-G) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM4BA1

The NM_002153.3(HSD17B2):c.1163A>G(p.Ter388Trpext*?) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.007 in 1,589,486 control chromosomes in the GnomAD database, including 270 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 0.019 ( 70 hom., cov: 32)

Exomes 𝑓: 0.0057 ( 200 hom. )

Consequence

HSD17B2
NM_002153.3 stop_lost

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.260

Variant links:

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 links:

HSD17B2-AS1 (HGNC:56281): (HSD17B2 antisense RNA 1)

HSD17B2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

PM4

Stoplost variant in NM_002153.3 Downstream stopcodon found after 444 codons.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD17B2	NM_002153.3 link	c.1163A>G	p.Ter388Trpext*?	stop_lost	Exon 5 of 5	ENST00000199936.9	NP_002144.1	P37059

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
HSD17B2	ENST00000199936.9 link	c.1163A>G	p.Ter388Trpext*?	stop_lost	Exon 5 of 5	1	NM_002153.3	ENSP00000199936.4	P37059
HSD17B2	ENST00000566838.2 link	c.*7259A>G		3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000456471.1	H3BRZ6
HSD17B2-AS1	ENST00000567021.1 link	n.44-27246T>C		intron_variant	Intron 1 of 3	5
HSD17B2	ENST00000568090.5 link	c.*94A>G		downstream_gene_variant		3		ENSP00000456529.1	H3BS44

Frequencies

GnomAD3 genomes

AF:

0.0193

AC:

2930

AN:

152206

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0548

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00583

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0504

Gnomad SAS

AF:

0.0497

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000514

Gnomad OTH

AF:

0.0139

GnomAD3 exomes

AF:

0.0127

AC:

2939

AN:

230874

Hom.:

AF XY:

0.0125

AC XY:

1553

AN XY:

124438

show subpopulations

Gnomad AFR exome

AF:

0.0568

Gnomad AMR exome

AF:

0.00292

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0468

Gnomad SAS exome

AF:

0.0382

Gnomad FIN exome

AF:

0.000245

Gnomad NFE exome

AF:

0.000787

Gnomad OTH exome

AF:

0.00799

GnomAD4 exome

AF:

0.00570

AC:

8191

AN:

1437162

Hom.:

200

Cov.:

AF XY:

0.00637

AC XY:

4541

AN XY:

712546

show subpopulations

Gnomad4 AFR exome

AF:

0.0581

Gnomad4 AMR exome

AF:

0.00333

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0415

Gnomad4 SAS exome

AF:

0.0375

Gnomad4 FIN exome

AF:

0.000171

Gnomad4 NFE exome

AF:

0.000680

Gnomad4 OTH exome

AF:

0.0112

GnomAD4 genome

AF:

0.0193

AC:

2941

AN:

152324

Hom.:

Cov.:

AF XY:

0.0197

AC XY:

1467

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.0550

Gnomad4 AMR

AF:

0.00575

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0500

Gnomad4 SAS

AF:

0.0498

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000515

Gnomad4 OTH

AF:

0.0151

Alfa

AF:

0.00525

Hom.:

Bravo

AF:

0.0201

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.0547

AC:

241

ESP6500EA

AF:

0.00116

AC:

ExAC

AF:

0.0133

AC:

1613

Asia WGS

AF:

0.0710

AC:

246

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.73

CADD

Benign

5.0

DANN

Benign

0.76

Eigen

Benign

0.13

Eigen_PC

Benign

-0.26

FATHMM_MKL

Benign

0.022

Vest4

0.061

GERP RS

0.67

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over