rs1119933

Variant names:

• chr16-82100178-C-T
• rs1119933
• ENST00000567021.2:n.44-28989G>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.44-28989G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,104 control chromosomes in the GnomAD database, including 5,521 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 0.24 (5521 hom., cov: 33)
• Consequence: HSD17B2-AS1 ENST00000567021.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 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.44-28989G>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36717 AN: 151986 Hom.: 5520 Cov.: 33

Gnomad AFR AF: 0.0712

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.241 AC: 36715 AN: 152104 Hom.: 5521 Cov.: 33 AF XY: 0.243 AC XY: 18095 AN XY: 74342

African (AFR) AF: 0.0710 AC: 2946 AN: 41504

American (AMR) AF: 0.220 AC: 3360 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3470

East Asian (EAS) AF: 0.105 AC: 545 AN: 5186

South Asian (SAS) AF: 0.370 AC: 1781 AN: 4820

European-Finnish (FIN) AF: 0.360 AC: 3795 AN: 10544

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.331 AC: 22468 AN: 67978

Other (OTH) AF: 0.253 AC: 534 AN: 2108

Alfa AF: 0.314 Hom.: 3341

Bravo AF: 0.220

Asia WGS AF: 0.265 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.2
DANN	Benign	0.85
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1119933; hg19: chr16-82133783;