rs11150438

Variant names:

• chr16-82106282-A-C
• rs11150438
• ENST00000567021.2:n.43+33307T>G

Your query was ambiguous. Multiple possible variants found:

• chr16-82106282-A-C
• chr16-82106282-A-G
• chr16-82106282-A-T

Variant summary

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

The ENST00000567021.2(HSD17B2-AS1):​n.43+33307T>G variant causes a intron 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 ENST00000567021.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 1 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=-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD17B2-AS1	ENST00000567021.2	n.43+33307T>G		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.625 AC: 25860 AN: 41406

American (AMR) AF: 0.701 AC: 10703 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 2944 AN: 3470

East Asian (EAS) AF: 0.480 AC: 2471 AN: 5150

South Asian (SAS) AF: 0.759 AC: 3639 AN: 4796

European-Finnish (FIN) AF: 0.931 AC: 9854 AN: 10586

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62406 AN: 67986

Other (OTH) AF: 0.796 AC: 1683 AN: 2114

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
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs11150438; hg19: chr16-82139887;