16-82102961-C-T

Variant names:

• chr16-82102961-C-T
• rs3887358
• ENST00000567021.1:n.44-31772G>A

Variant summary

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

The ENST00000567021.1(HSD17B2-AS1):​n.44-31772G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,088 control chromosomes in the GnomAD database, including 49,060 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 0.79 (49060 hom., cov: 31)
• Consequence: HSD17B2-AS1 ENST00000567021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

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 = 0.889 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.44-31772G>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120773 AN: 151970 Hom.: 49025 Cov.: 31

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.795 AC: 120857 AN: 152088 Hom.: 49060 Cov.: 31 AF XY: 0.790 AC XY: 58733 AN XY: 74334

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.807

Alfa AF: 0.855 Hom.: 32842

Bravo AF: 0.777

Asia WGS AF: 0.672 AC: 2340 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	1.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3887358; hg19: chr16-82136566;