dbSNP rs2830: HSD17B1-AS1:n.2297C>T (chr17-42552545-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_144402.1(HSD17B1-AS1):n.2258C>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
NR_144402.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.257

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 made for transcript

Verdict is Benign. Variant got -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	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD17B1-AS1	ENST00000590513.3 link	n.2297C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
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

Gnomad4 AFR exome

AF:

0.645

Gnomad4 AMR exome

AF:

0.516

Gnomad4 ASJ exome

AF:

0.347

Gnomad4 EAS exome

AF:

0.402

Gnomad4 SAS exome

AF:

0.594

Gnomad4 FIN exome

AF:

0.493

Gnomad4 NFE exome

AF:

0.527

Gnomad4 OTH exome

AF:

0.494

GnomAD4 genome

AF:

0.574

AC:

87284

AN:

151986

Hom.:

25517

Cov.:

AF XY:

0.570

AC XY:

42371

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.683

Gnomad4 AMR

AF:

0.502

Gnomad4 ASJ

AF:

0.391

Gnomad4 EAS

AF:

0.438

Gnomad4 SAS

AF:

0.640

Gnomad4 FIN

AF:

0.530

Gnomad4 NFE

AF:

0.550

Gnomad4 OTH

AF:

0.526

Alfa

AF:

0.558

Hom.:

2966

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

DANN

Benign

0.43

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