rs4545339

Variant names:

• chr1-209739397-C-G
• rs4545339
• ENST00000441672.2:n.169-15253G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-209739397-C-G
• chr1-209739397-C-T

Variant summary

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

The ENST00000441672.2(HSD11B1-AS1):​n.169-15253G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.052 in 152,144 control chromosomes in the GnomAD database, including 637 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 0.052 (637 hom., cov: 32)
• Consequence: HSD11B1-AS1 ENST00000441672.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 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_134510.1		n.66+3100G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD11B1-AS1	ENST00000441672.2	TSL:3	n.169-15253G>C		intron	N/A
	HSD11B1-AS1	ENST00000774900.1		n.121+18079G>C		intron	N/A
	HSD11B1-AS1	ENST00000774901.1		n.141+3100G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0521 AC: 7917 AN: 152026 Hom.: 634 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.0124

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0520 AC: 7916 AN: 152144 Hom.: 637 Cov.: 32 AF XY: 0.0574 AC XY: 4269 AN XY: 74388

African (AFR) AF: 0.0472 AC: 1960 AN: 41518

American (AMR) AF: 0.184 AC: 2807 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1538 AN: 5130

South Asian (SAS) AF: 0.0985 AC: 474 AN: 4814

European-Finnish (FIN) AF: 0.0124 AC: 131 AN: 10590

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.0123 AC: 837 AN: 68018

Other (OTH) AF: 0.0416 AC: 88 AN: 2114

Alfa AF: 0.00356 Hom.: 0

Bravo AF: 0.0648

Asia WGS AF: 0.160 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		-0.0060

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: rs4545339;

hg19: chr1-209912742;