Genetic Variant PLS3-AS1:n.210-12929C>T (chrX-115540697-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

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

The ENST00000606397.1(PLS3-AS1):n.210-12929C>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
ENST00000606397.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.112

Publications

0 publications found

Variant links:

Genes affected

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

PLS3-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLS3-AS1	NR_110383.1 link	n.234-12929C>T		intron_variant	Intron 2 of 4
PLS3-AS1	NR_110384.1 link	n.234-20986C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLS3-AS1	ENST00000606397.1 link	n.210-12929C>T		intron_variant	Intron 2 of 3	4
PLS3-AS1	ENST00000607680.5 link	n.234-20986C>T		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.501

AC:

55818

AN:

111479

Hom.:

10119

Cov.:

show subpopulations

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.:

AF XY:

0.508

AC XY:

17149

AN XY:

33781

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

983

1966

2949

3932

4915

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

550

1100

1650

2200

2750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

PhyloP100

0.11

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over