16-82106956-C-T

Variant names:

• chr16-82106956-C-T
• rs9923501
• ENST00000567021.2:n.43+32633G>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.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 ENST00000567021.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567021.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B2-AS1	ENST00000567021.2	TSL:5	n.43+32633G>A		intron	N/A

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

African (AFR) AF: 0.799 AC: 33096 AN: 41416

American (AMR) AF: 0.731 AC: 11152 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 3202 AN: 3468

East Asian (EAS) AF: 0.699 AC: 3593 AN: 5140

South Asian (SAS) AF: 0.866 AC: 4177 AN: 4824

European-Finnish (FIN) AF: 0.946 AC: 10007 AN: 10582

Middle Eastern (MID) AF: 0.846 AC: 247 AN: 292

European-Non Finnish (NFE) AF: 0.937 AC: 63740 AN: 67992

Other (OTH) AF: 0.866 AC: 1830 AN: 2114

Alfa AF: 0.915 Hom.: 196727

Bravo AF: 0.848

Asia WGS AF: 0.806 AC: 2803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.56
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs9923501; hg19: chr16-82140561;