16-82103606-C-G

Variant names:

• chr16-82103606-C-G
• rs989019
• ENST00000567021.2:n.44-32417G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000567021.2(HSD17B2-AS1):​n.44-32417G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,990 control chromosomes in the GnomAD database, including 18,456 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 0.49 (18456 hom., cov: 32)
• Consequence: HSD17B2-AS1 ENST00000567021.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 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	ENST00000567021.2	n.44-32417G>C		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74567 AN: 151872 Hom.: 18442 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.491 AC: 74618 AN: 151990 Hom.: 18456 Cov.: 32 AF XY: 0.487 AC XY: 36183 AN XY: 74272

African (AFR) AF: 0.477 AC: 19799 AN: 41478

American (AMR) AF: 0.442 AC: 6753 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1847 AN: 3472

East Asian (EAS) AF: 0.432 AC: 2236 AN: 5170

South Asian (SAS) AF: 0.364 AC: 1748 AN: 4808

European-Finnish (FIN) AF: 0.501 AC: 5279 AN: 10540

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35256 AN: 67940

Other (OTH) AF: 0.508 AC: 1070 AN: 2106

Alfa AF: 0.354 Hom.: 900

Bravo AF: 0.489

Asia WGS AF: 0.386 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.051
DANN	Benign	0.56
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs989019; hg19: chr16-82137211;