rs10514527

Variant names:

• chr16-82104037-A-C
• rs10514527
• ENST00000567021.1:n.44-32848T>G

Your query was ambiguous. Multiple possible variants found:

• chr16-82104037-A-C
• chr16-82104037-A-G

Variant summary

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

The ENST00000567021.1(HSD17B2-AS1):​n.44-32848T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,094 control chromosomes in the GnomAD database, including 6,529 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 0.26 (6529 hom., cov: 32)
• Consequence: HSD17B2-AS1 ENST00000567021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 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.44-32848T>G		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39656 AN: 151976 Hom.: 6529 Cov.: 32

Gnomad AFR AF: 0.0775

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.261 AC: 39662 AN: 152094 Hom.: 6529 Cov.: 32 AF XY: 0.262 AC XY: 19446 AN XY: 74354

Gnomad4 AFR AF: 0.0774

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.0612

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.263

Alfa AF: 0.332 Hom.: 13199

Bravo AF: 0.239

Asia WGS AF: 0.211 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514527; hg19: chr16-82137642;