chr17-42552545-G-T

Variant names:

• chr17-42552545-G-T
• rs2830
• ENST00000590513.3:n.2297C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 33 publications found

Genes affected

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

ENSG00000266929 (HGNC:):

ACMG classification

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000590513.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B1-AS1	NR_144402.1		n.2258C>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B1-AS1	ENST00000590513.3	TSL:6	n.2297C>A		non_coding_transcript_exon	Exon 1 of 1
	HSD17B1-AS1	ENST00000803215.1		n.1283C>A		non_coding_transcript_exon	Exon 2 of 2
	HSD17B1-AS1	ENST00000803216.1		n.1223C>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 88060 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 45894

African (AFR) AF: 0.00 AC: 0 AN: 2432

American (AMR) AF: 0.00 AC: 0 AN: 4358

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2560

East Asian (EAS) AF: 0.00 AC: 0 AN: 4522

South Asian (SAS) AF: 0.00 AC: 0 AN: 11098

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3768

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 346

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 54088

Other (OTH) AF: 0.00 AC: 0 AN: 4888

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.83
DANN	Benign	0.42
PhyloP100		-0.26
PromoterAI		-0.030	Neutral

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

Other links and lift over

dbSNP: rs2830; hg19: chr17-40704563;