Genetic Variant ENST00000590513.3:n.2297C>T (chr17-42552545-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000590513.3(HSD17B1-AS1):n.2297C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 239,470 control chromosomes in the GnomAD database, including 37,952 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 0.57 ( 25517 hom., cov: 32)

Exomes 𝑓: 0.52 ( 12435 hom. )

Consequence

HSD17B1-AS1
ENST00000590513.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.257

Publications

33 publications found

Variant links:

Genes affected

HSD17B1-AS1 (HGNC:55314): (HSD17B1 antisense RNA 1)

HSD17B1-AS1 links:

ENSG00000266929 (HGNC:):

ENSG00000266929 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD17B1-AS1	NR_144402.1 link	n.2258C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HSD17B1-AS1	ENST00000590513.3 link	n.2297C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
HSD17B1-AS1	ENST00000803215.1 link	n.1283C>T	non_coding_transcript_exon_variant	Exon 2 of 2
HSD17B1-AS1	ENST00000803216.1 link	n.1223C>T	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000266929	ENST00000585572.1 link	n.380-9074G>A	intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes

AF:

0.574

AC:

87198

AN:

151868

Hom.:

25487

Cov.:

show subpopulations

Gnomad AFR

AF:

0.683

Gnomad AMI

AF:

0.465

Gnomad AMR

AF:

0.501

Gnomad ASJ

AF:

0.391

Gnomad EAS

AF:

0.438

Gnomad SAS

AF:

0.641

Gnomad FIN

AF:

0.530

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.550

Gnomad OTH

AF:

0.522

GnomAD4 exome

AF:

0.522

AC:

45705

AN:

87484

Hom.:

12435

Cov.:

AF XY:

0.525

AC XY:

23922

AN XY:

45582

show subpopulations

African (AFR)

AF:

0.645

AC:

1555

AN:

2410

American (AMR)

AF:

0.516

AC:

2241

AN:

4342

Ashkenazi Jewish (ASJ)

AF:

0.347

AC:

887

AN:

2554

East Asian (EAS)

AF:

0.402

AC:

1809

AN:

4500

South Asian (SAS)

AF:

0.594

AC:

6553

AN:

11024

European-Finnish (FIN)

AF:

0.493

AC:

1850

AN:

3750

Middle Eastern (MID)

AF:

0.372

AC:

128

AN:

344

European-Non Finnish (NFE)

AF:

0.527

AC:

28284

AN:

53710

Other (OTH)

AF:

0.494

AC:

2398

AN:

4850

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

940

1880

2820

3760

4700

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

266

532

798

1064

1330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.574

AC:

87284

AN:

151986

Hom.:

25517

Cov.:

AF XY:

0.570

AC XY:

42371

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.683

AC:

28295

AN:

41448

American (AMR)

AF:

0.502

AC:

7663

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.391

AC:

1353

AN:

3464

East Asian (EAS)

AF:

0.438

AC:

2264

AN:

5168

South Asian (SAS)

AF:

0.640

AC:

3087

AN:

4824

European-Finnish (FIN)

AF:

0.530

AC:

5593

AN:

10558

Middle Eastern (MID)

AF:

0.425

AC:

125

AN:

294

European-Non Finnish (NFE)

AF:

0.550

AC:

37371

AN:

67940

Other (OTH)

AF:

0.526

AC:

1109

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

1804

3609

5413

7218

9022

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

746

1492

2238

2984

3730

<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:

0.563

Hom.:

3140

Bravo

AF:

0.573

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.0

(source)

DANN

Benign

0.43

PhyloP100

-0.26

PromoterAI

0.012

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over