rs17317033

chr1-209683281-A-C

Variant summary

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

The NR_134510.1(HSD11B1-AS1):n.67-20220T>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 0.0894 in 152,248 control chromosomes in the GnomAD database, including 681 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 0.089 (681 hom., cov: 32)
• Consequence: HSD11B1-AS1 NR_134510.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

Genes affected

HSD11B1-AS1 (HGNC:54053): (HSD11B1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD11B1-AS1	NR_134510.1	n.67-20220T>G		intron_variant, non_coding_transcript_variant
HSD11B1-AS1	NR_134509.1	n.97-20220T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD11B1-AS1	ENST00000441672.1	n.97-20220T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0895 AC: 13616 AN: 152130 Hom.: 683 Cov.: 32

Gnomad AFR AF: 0.0626

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0733

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0957

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

GnomAD4 genome AF: 0.0894 AC: 13618 AN: 152248 Hom.: 681 Cov.: 32 AF XY: 0.0905 AC XY: 6737 AN XY: 74440

Gnomad4 AFR AF: 0.0626

Gnomad4 AMR AF: 0.0731

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0952

Alfa AF: 0.105 Hom.: 858

Bravo AF: 0.0821

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.55
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17317033; hg19: chr1-209856626;