ENST00000567021.2:n.44-31772G>A

Variant names:

• chr16-82102961-C-T
• rs3887358
• ENST00000567021.2:n.44-31772G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000567021.2(HSD17B2-AS1):​n.44-31772G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,088 control chromosomes in the GnomAD database, including 49,060 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 0.79 (49060 hom., cov: 31)
• Consequence: HSD17B2-AS1 ENST00000567021.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD17B2-AS1	ENST00000567021.2	n.44-31772G>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120773 AN: 151970 Hom.: 49025 Cov.: 31

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.795 AC: 120857 AN: 152088 Hom.: 49060 Cov.: 31 AF XY: 0.790 AC XY: 58733 AN XY: 74334

African (AFR) AF: 0.663 AC: 27498 AN: 41446

American (AMR) AF: 0.698 AC: 10660 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2990 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3165 AN: 5154

South Asian (SAS) AF: 0.732 AC: 3520 AN: 4810

European-Finnish (FIN) AF: 0.884 AC: 9371 AN: 10596

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60885 AN: 68024

Other (OTH) AF: 0.807 AC: 1702 AN: 2110

Alfa AF: 0.850 Hom.: 117036

Bravo AF: 0.777

Asia WGS AF: 0.672 AC: 2340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs3887358; hg19: chr16-82136566;