16-82106956-C-T

Variant summary

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

The ENST00000567021.1(HSD17B2-AS1):n.43+32633G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 152,000 control chromosomes in the GnomAD database, including 57,850 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 0.87 (57850 hom., cov: 33)
• Consequence: HSD17B2-AS1 ENST00000567021.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

Genes affected

HSD17B2-AS1 (HGNC:56281): (HSD17B2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B2-AS1	ENST00000567021.1	n.43+32633G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.868 AC: 131792 AN: 151882 Hom.: 57799 Cov.: 33

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.866

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.868 AC: 131895 AN: 152000 Hom.: 57850 Cov.: 33 AF XY: 0.864 AC XY: 64186 AN XY: 74298

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.946

Gnomad4 NFE AF: 0.937

Gnomad4 OTH AF: 0.866

Alfa AF: 0.925 Hom.: 84001

Bravo AF: 0.848

Asia WGS AF: 0.806 AC: 2803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.11
Dann	Benign	0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9923501; hg19: chr16-82140561;