rs11150438

chr16-82106282-A-Cchr16-82106282-A-Gchr16-82106282-A-T

Variant summary

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

The ENST00000567021.1(HSD17B2-AS1):n.43+33307T>G 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 0.794 in 151,982 control chromosomes in the GnomAD database, including 49,584 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 (49584 hom., cov: 30)
• Consequence: HSD17B2-AS1 ENST00000567021.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.912 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.43+33307T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120556 AN: 151864 Hom.: 49552 Cov.: 30

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.794 AC: 120635 AN: 151982 Hom.: 49584 Cov.: 30 AF XY: 0.790 AC XY: 58650 AN XY: 74286

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.796

Alfa AF: 0.859 Hom.: 5547

Bravo AF: 0.769

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11150438; hg19: chr16-82139887;