rs10514524

chr16-82101790-T-Achr16-82101790-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B2-AS1	ENST00000567021.1	n.44-30601A>T		intron_variant, non_coding_transcript_variant		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;