rs11643002

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000567021.1(HSD17B2-AS1):​n.44-33660T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,016 control chromosomes in the GnomAD database, including 9,491 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 0.35 ( 9491 hom., cov: 32)

Consequence

HSD17B2-AS1
ENST00000567021.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.41
Variant links:
Genes affected
HSD17B2-AS1 (HGNC:56281): (HSD17B2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.439 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-AS1ENST00000567021.1 linkn.44-33660T>C intron_variant Intron 1 of 3 5

Frequencies

GnomAD3 genomes
AF:
0.346
AC:
52515
AN:
151898
Hom.:
9482
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.297
Gnomad AMI
AF:
0.370
Gnomad AMR
AF:
0.273
Gnomad ASJ
AF:
0.276
Gnomad EAS
AF:
0.151
Gnomad SAS
AF:
0.454
Gnomad FIN
AF:
0.425
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.391
Gnomad OTH
AF:
0.325
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.346
AC:
52549
AN:
152016
Hom.:
9491
Cov.:
32
AF XY:
0.347
AC XY:
25772
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.297
Gnomad4 AMR
AF:
0.273
Gnomad4 ASJ
AF:
0.276
Gnomad4 EAS
AF:
0.150
Gnomad4 SAS
AF:
0.455
Gnomad4 FIN
AF:
0.425
Gnomad4 NFE
AF:
0.391
Gnomad4 OTH
AF:
0.328
Alfa
AF:
0.364
Hom.:
16855
Bravo
AF:
0.328
Asia WGS
AF:
0.334
AC:
1162
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.1
DANN
Benign
0.38

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11643002; hg19: chr16-82138454; API