chr1-209685108-A-G

Variant names:

• chr1-209685108-A-G
• rs846908
• ENST00000441672.2:n.284-22047T>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.284-22047T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 152,356 control chromosomes in the GnomAD database, including 70,695 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 0.96 (70695 hom., cov: 32)
• Consequence: HSD11B1-AS1 ENST00000441672.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 10 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.985 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.97-22047T>C		intron	N/A
	HSD11B1-AS1	NR_134510.1		n.67-22047T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD11B1-AS1	ENST00000441672.2	TSL:3	n.284-22047T>C		intron	N/A
	HSD11B1-AS1	ENST00000774900.1		n.122-22047T>C		intron	N/A
	HSD11B1-AS1	ENST00000774901.1		n.142-22047T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.961 AC: 146361 AN: 152238 Hom.: 70636 Cov.: 32

Gnomad AFR AF: 0.993

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.987

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.966

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

GnomAD4 genome AF: 0.961 AC: 146478 AN: 152356 Hom.: 70695 Cov.: 32 AF XY: 0.958 AC XY: 71362 AN XY: 74494

African (AFR) AF: 0.993 AC: 41303 AN: 41586

American (AMR) AF: 0.891 AC: 13638 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.987 AC: 3426 AN: 3472

East Asian (EAS) AF: 0.717 AC: 3716 AN: 5180

South Asian (SAS) AF: 0.917 AC: 4426 AN: 4826

European-Finnish (FIN) AF: 0.983 AC: 10449 AN: 10626

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66303 AN: 68046

Other (OTH) AF: 0.966 AC: 2042 AN: 2114

Alfa AF: 0.965 Hom.: 257464

Bravo AF: 0.957

Asia WGS AF: 0.844 AC: 2935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.67
PhyloP100		-0.52

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: rs846908;

hg19: chr1-209858453;