chr16-82101790-T-A

Variant names:

• chr16-82101790-T-A
• rs10514524
• ENST00000567021.2:n.44-30601A>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.44-30601A>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 ENST00000567021.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD17B2-AS1	ENST00000567021.2	TSL:5	n.44-30601A>T		intron	N/A

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

African (AFR) AF: 0.241 AC: 10005 AN: 41496

American (AMR) AF: 0.395 AC: 6026 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1713 AN: 3468

East Asian (EAS) AF: 0.389 AC: 2005 AN: 5160

South Asian (SAS) AF: 0.304 AC: 1466 AN: 4822

European-Finnish (FIN) AF: 0.478 AC: 5048 AN: 10550

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 33004 AN: 67942

Other (OTH) AF: 0.439 AC: 926 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs10514524; hg19: chr16-82135395;