rs10514524

Variant names:

• chr16-82101790-T-A
• rs10514524
• ENST00000567021.1:n.44-30601A>T

Your query was ambiguous. Multiple possible variants found:

• chr16-82101790-T-A
• chr16-82101790-T-G

Variant summary

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

The ENST00000567021.1(HSD17B2-AS1):​n.44-30601A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,016 control chromosomes in the GnomAD database, including 13,065 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 0.40 (13065 hom., cov: 32)
• Consequence: HSD17B2-AS1 ENST00000567021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 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.44-30601A>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60766 AN: 151898 Hom.: 13063 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.400 AC: 60776 AN: 152016 Hom.: 13065 Cov.: 32 AF XY: 0.397 AC XY: 29507 AN XY: 74292

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.439

Alfa AF: 0.441 Hom.: 1910

Bravo AF: 0.392

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514524; hg19: chr16-82135395;