rs11649253

chr16-82103750-A-G

Variant summary

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

The ENST00000567021.1(HSD17B2-AS1):n.44-32561T>C 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 0.0259 in 152,276 control chromosomes in the GnomAD database, including 60 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 0.026 (60 hom., cov: 32)
• Consequence: HSD17B2-AS1 ENST00000567021.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0545 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.44-32561T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0259 AC: 3939 AN: 152158 Hom.: 60 Cov.: 32

Gnomad AFR AF: 0.00758

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.0458

Gnomad SAS AF: 0.0597

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0259 AC: 3941 AN: 152276 Hom.: 60 Cov.: 32 AF XY: 0.0262 AC XY: 1950 AN XY: 74458

Gnomad4 AFR AF: 0.00755

Gnomad4 AMR AF: 0.0203

Gnomad4 ASJ AF: 0.0352

Gnomad4 EAS AF: 0.0454

Gnomad4 SAS AF: 0.0601

Gnomad4 FIN AF: 0.0232

Gnomad4 NFE AF: 0.0342

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0263 Hom.: 7

Bravo AF: 0.0235

Asia WGS AF: 0.0790 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	6.1
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11649253; hg19: chr16-82137355;