ENST00000567021.2:n.44-32561T>C

Variant names:

• chr16-82103750-A-G
• rs11649253
• ENST00000567021.2:n.44-32561T>C

Variant summary

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

The ENST00000567021.2(HSD17B2-AS1):​n.44-32561T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0259 in 152,276 control chromosomes in the GnomAD database, including 60 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 0.026 (60 hom., cov: 32)
• Consequence: HSD17B2-AS1 ENST00000567021.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• 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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0545 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.44-32561T>C		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0259 AC: 3939 AN: 152158 Hom.: 60 Cov.: 32

Gnomad AFR AF: 0.00758

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.0458

Gnomad SAS AF: 0.0597

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0259 AC: 3941 AN: 152276 Hom.: 60 Cov.: 32 AF XY: 0.0262 AC XY: 1950 AN XY: 74458

African (AFR) AF: 0.00755 AC: 314 AN: 41564

American (AMR) AF: 0.0203 AC: 311 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3470

East Asian (EAS) AF: 0.0454 AC: 235 AN: 5180

South Asian (SAS) AF: 0.0601 AC: 290 AN: 4822

European-Finnish (FIN) AF: 0.0232 AC: 246 AN: 10606

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0342 AC: 2326 AN: 68020

Other (OTH) AF: 0.0279 AC: 59 AN: 2114

Alfa AF: 0.0263 Hom.: 7

Bravo AF: 0.0235

Asia WGS AF: 0.0790 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.1
DANN	Benign	0.80
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs11649253; hg19: chr16-82137355;