16-82110254-C-T

Variant names:

• chr16-82110254-C-T
• rs10514530
• ENST00000567021.1:n.43+29335G>A

Variant summary

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

The ENST00000567021.1(HSD17B2-AS1):​n.43+29335G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,196 control chromosomes in the GnomAD database, including 744 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 0.067 (744 hom., cov: 32)
• Consequence: HSD17B2-AS1 ENST00000567021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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.43+29335G>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0666 AC: 10122 AN: 152078 Hom.: 744 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0319

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0666 AC: 10133 AN: 152196 Hom.: 744 Cov.: 32 AF XY: 0.0646 AC XY: 4809 AN XY: 74414

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0319

Gnomad4 ASJ AF: 0.0753

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0226

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.0155

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0278 Hom.: 159

Bravo AF: 0.0752

Asia WGS AF: 0.0900 AC: 313 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
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: rs10514530; hg19: chr16-82143859;