rs2830

chr17-42552545-G-Achr17-42552545-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

Genes affected

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

ACMG classification

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/exons	MANE	UniProt
HSD17B1-AS1	NR_144402.1	n.2258C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B1-AS1	ENST00000590513.3	n.2297C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87198 AN: 151868 Hom.: 25487 Cov.: 32

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.: 0 AF XY: 0.525 AC XY: 23922 AN XY: 45582

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.: 32 AF XY: 0.570 AC XY: 42371 AN XY: 74302

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

Other links and lift over

dbSNP: rs2830; hg19: chr17-40704563;