rs11643002

Variant names:

• chr16-82104849-A-G
• rs11643002
• ENST00000567021.2:n.44-33660T>C

Your query was ambiguous. Multiple possible variants found:

• chr16-82104849-A-G
• chr16-82104849-A-T

Variant summary

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

The ENST00000567021.2(HSD17B2-AS1):​n.44-33660T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,016 control chromosomes in the GnomAD database, including 9,491 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 0.35 (9491 hom., cov: 32)
• Consequence: HSD17B2-AS1 ENST00000567021.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.439 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B2-AS1	ENST00000567021.2	TSL:5	n.44-33660T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52515 AN: 151898 Hom.: 9482 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.346 AC: 52549 AN: 152016 Hom.: 9491 Cov.: 32 AF XY: 0.347 AC XY: 25772 AN XY: 74294

African (AFR) AF: 0.297 AC: 12291 AN: 41432

American (AMR) AF: 0.273 AC: 4171 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 959 AN: 3472

East Asian (EAS) AF: 0.150 AC: 777 AN: 5182

South Asian (SAS) AF: 0.455 AC: 2187 AN: 4808

European-Finnish (FIN) AF: 0.425 AC: 4494 AN: 10562

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26571 AN: 67960

Other (OTH) AF: 0.328 AC: 693 AN: 2110

Alfa AF: 0.370 Hom.: 40785

Bravo AF: 0.328

Asia WGS AF: 0.334 AC: 1162 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	1.1
DANN	Benign	0.38
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs11643002; hg19: chr16-82138454;