rs2843586

Positions:

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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_110384.1(PLS3-AS1):​n.234-20986C>T variant causes a intron, non coding transcript 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 NR_110384.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLS3-AS1	NR_110384.1	n.234-20986C>T		intron_variant, non_coding_transcript_variant
PLS3-AS1	NR_110383.1	n.234-12929C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLS3-AS1	ENST00000607680.5	n.234-20986C>T		intron_variant, non_coding_transcript_variant		2
PLS3-AS1	ENST00000606397.1	n.210-12929C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.501 AC: 55818 AN: 111479 Hom.: 10119 Cov.: 24 AF XY: 0.508 AC XY: 17133 AN XY: 33717

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

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.536

Alfa AF: 0.530 Hom.: 3767

Bravo AF: 0.481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2843586; hg19: chrX-114775033;