chr1-209678552-A-G

Variant names:

• chr1-209678552-A-G
• rs4393158
• ENST00000441672.2:n.284-15491T>C

Variant summary

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

The ENST00000441672.2(HSD11B1-AS1):​n.284-15491T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 152,236 control chromosomes in the GnomAD database, including 67,422 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 0.94 (67422 hom., cov: 31)
• Consequence: HSD11B1-AS1 ENST00000441672.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 8 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.979 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD11B1-AS1	NR_134509.1		n.97-15491T>C		intron	N/A
	HSD11B1-AS1	NR_134510.1		n.67-15491T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD11B1-AS1	ENST00000441672.2	TSL:3	n.284-15491T>C		intron	N/A
	HSD11B1-AS1	ENST00000774900.1		n.122-15491T>C		intron	N/A
	HSD11B1-AS1	ENST00000774901.1		n.142-15491T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142775 AN: 152118 Hom.: 67364 Cov.: 31

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.939 AC: 142892 AN: 152236 Hom.: 67422 Cov.: 31 AF XY: 0.935 AC XY: 69583 AN XY: 74424

African (AFR) AF: 0.987 AC: 41021 AN: 41548

American (AMR) AF: 0.880 AC: 13455 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3390 AN: 3472

East Asian (EAS) AF: 0.640 AC: 3299 AN: 5154

South Asian (SAS) AF: 0.915 AC: 4408 AN: 4818

European-Finnish (FIN) AF: 0.931 AC: 9883 AN: 10610

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64292 AN: 68026

Other (OTH) AF: 0.945 AC: 1995 AN: 2112

Alfa AF: 0.940 Hom.: 143926

Bravo AF: 0.937

Asia WGS AF: 0.812 AC: 2824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.38
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs4393158; hg19: chr1-209851897;