16-82106956-C-T

Variant names:

• chr16-82106956-C-T
• rs9923501
• ENST00000567021.1:n.43+32633G>A

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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD17B2-AS1	ENST00000567021.1	n.43+32633G>A		intron_variant	Intron 1 of 3	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;