rs17317033

Variant names:

• chr1-209683281-A-C
• rs17317033
• ENST00000441672.2:n.284-20220T>G

Variant summary

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

The ENST00000441672.2(HSD11B1-AS1):​n.284-20220T>G variant causes a intron 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 ENST00000441672.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441672.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD11B1-AS1	NR_134509.1		n.97-20220T>G		intron	N/A
	HSD11B1-AS1	NR_134510.1		n.67-20220T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD11B1-AS1	ENST00000441672.2	TSL:3	n.284-20220T>G		intron	N/A
	HSD11B1-AS1	ENST00000774900.1		n.122-20220T>G		intron	N/A
	HSD11B1-AS1	ENST00000774901.1		n.142-20220T>G		intron	N/A

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

African (AFR) AF: 0.0626 AC: 2603 AN: 41556

American (AMR) AF: 0.0731 AC: 1118 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3470

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5186

South Asian (SAS) AF: 0.107 AC: 517 AN: 4822

European-Finnish (FIN) AF: 0.119 AC: 1259 AN: 10600

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7318 AN: 68004

Other (OTH) AF: 0.0952 AC: 201 AN: 2112

Alfa AF: 0.0985 Hom.: 1184

Bravo AF: 0.0821

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.55
DANN	Benign	0.70
PhyloP100		-0.59

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17317033;

hg19: chr1-209856626;