rs2843586

Variant names:

• chrX-115540697-G-A
• rs2843586
• ENST00000606397.1:n.210-12929C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-115540697-G-A
• chrX-115540697-G-C
• chrX-115540697-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000607680.5(PLS3-AS1):​n.234-20986C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.50 (10120 hom., 17149 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: PLS3-AS1 ENST00000607680.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 0 publications found

Genes affected

PLS3-AS1 (HGNC:50343): (PLS3 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607680.5. 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
	PLS3-AS1	NR_110383.1		n.234-12929C>T		intron	N/A
	PLS3-AS1	NR_110384.1		n.234-20986C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLS3-AS1	ENST00000606397.1	TSL:4	n.210-12929C>T		intron	N/A
	PLS3-AS1	ENST00000607680.5	TSL:2	n.234-20986C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 55818 AN: 111479 Hom.: 10119 Cov.: 24

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.498

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.535

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.501 AC: 55834 AN: 111533 Hom.: 10120 Cov.: 24 AF XY: 0.508 AC XY: 17149 AN XY: 33781

African (AFR) AF: 0.320 AC: 9879 AN: 30841

American (AMR) AF: 0.488 AC: 5185 AN: 10622

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 1661 AN: 2632

East Asian (EAS) AF: 0.517 AC: 1784 AN: 3452

South Asian (SAS) AF: 0.649 AC: 1724 AN: 2657

European-Finnish (FIN) AF: 0.654 AC: 3911 AN: 5983

Middle Eastern (MID) AF: 0.486 AC: 104 AN: 214

European-Non Finnish (NFE) AF: 0.577 AC: 30561 AN: 52953

Other (OTH) AF: 0.536 AC: 807 AN: 1505

Alfa AF: 0.530 Hom.: 3767

Bravo AF: 0.481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2843586; hg19: chrX-114775033;