16-82099387-A-G

Variant names:

• chr16-82099387-A-G
• rs996752
• ENST00000567021.1:n.44-28198T>C

Variant summary

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

The ENST00000567021.1(HSD17B2-AS1):​n.44-28198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,106 control chromosomes in the GnomAD database, including 8,239 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 0.32 (8239 hom., cov: 32)
• Consequence: HSD17B2-AS1 ENST00000567021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

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 (SAS) allele frequency at 95% confidence interval = 0.473 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.44-28198T>C		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49124 AN: 151988 Hom.: 8227 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.323 AC: 49153 AN: 152106 Hom.: 8239 Cov.: 32 AF XY: 0.325 AC XY: 24196 AN XY: 74372

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.306

Alfa AF: 0.346 Hom.: 18662

Bravo AF: 0.307

Asia WGS AF: 0.404 AC: 1405 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	0.074
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs996752; hg19: chr16-82132992;