Genetic Variant HSD17B1-AS1:n.2297C>A (chr17-42552545-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000590513.3(HSD17B1-AS1):n.2297C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

88060

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

45894

African (AFR)

AF:

0.00

AC:

AN:

2432

American (AMR)

AF:

0.00

AC:

AN:

4358

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2560

East Asian (EAS)

AF:

0.00

AC:

AN:

4522

South Asian (SAS)

AF:

0.00

AC:

AN:

11098

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3768

Middle Eastern (MID)

AF:

0.00

AC:

AN:

346

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

54088

Other (OTH)

AF:

0.00

AC:

AN:

4888

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.83

(source)

DANN

Benign

0.42

PhyloP100

-0.26

PromoterAI

-0.030

Neutral

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over