dbSNP rs10514527: HSD17B2-AS1:n.44-32848T>G (chr16-82104037-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000567021.2(HSD17B2-AS1):n.44-32848T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,094 control chromosomes in the GnomAD database, including 6,529 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 0.26 ( 6529 hom., cov: 32)

Consequence

HSD17B2-AS1
ENST00000567021.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.20

Publications

8 publications found

Variant links:

Genes affected

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

HSD17B2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD17B2-AS1	ENST00000567021.2 link	n.44-32848T>G		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39656

AN:

151976

Hom.:

6529

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0775

Gnomad AMI

AF:

0.370

Gnomad AMR

AF:

0.233

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.0614

Gnomad SAS

AF:

0.363

Gnomad FIN

AF:

0.393

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.365

Gnomad OTH

AF:

0.261

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

GnomAD4 genome

AF:

0.261

AC:

39662

AN:

152094

Hom.:

6529

Cov.:

AF XY:

0.262

AC XY:

19446

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.0774

AC:

3213

AN:

41512

American (AMR)

AF:

0.233

AC:

3563

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.267

AC:

927

AN:

3468

East Asian (EAS)

AF:

0.0612

AC:

317

AN:

5182

South Asian (SAS)

AF:

0.363

AC:

1753

AN:

4824

European-Finnish (FIN)

AF:

0.393

AC:

4147

AN:

10546

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.365

AC:

24789

AN:

67970

Other (OTH)

AF:

0.263

AC:

555

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1369

2738

4108

5477

6846

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

426

852

1278

1704

2130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.328

Hom.:

17934

Bravo

AF:

0.239

Asia WGS

AF:

0.211

AC:

737

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.8

(source)

DANN

Benign

0.64

PhyloP100

1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over