dbSNP rs5945431: PLXNA3:c.*688G>A (chrX-154473373-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017514.5(PLXNA3):c.*688G>A variant causes a 3 prime UTR 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 0.76 ( 23764 hom., 25368 hem., cov: 24)

Exomes 𝑓: 0.88 ( 93 hom. 131 hem. )

Failed GnomAD Quality Control

Consequence

PLXNA3
NM_017514.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Publications

5 publications found

Variant links:

Genes affected

PLXNA3 (HGNC:9101): (plexin A3) This gene encodes a member of the plexin class of proteins. The encoded protein is a class 3 semaphorin receptor, and may be involved in cytoskeletal remodeling and as well as apoptosis. Studies of a similar gene in zebrafish suggest that it is important for axon pathfinding in the developing nervous system. This gene may be associated with tumor progression. [provided by RefSeq, Aug 2013]

PLXNA3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017514.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLXNA3	NM_017514.5	MANE Select	c.*688G>A		3_prime_UTR	Exon 33 of 33	NP_059984.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PLXNA3	ENST00000369682.4	TSL:1 MANE Select	c.*688G>A	3_prime_UTR	Exon 33 of 33	ENSP00000358696.3
PLXNA3	ENST00000937806.1		c.*688G>A	3_prime_UTR	Exon 33 of 33	ENSP00000607865.1
PLXNA3	ENST00000955276.1		c.*688G>A	3_prime_UTR	Exon 33 of 33	ENSP00000625335.1

Frequencies

GnomAD3 genomes

AF:

0.765

AC:

84912

AN:

111021

Hom.:

23763

Cov.:

show subpopulations

Gnomad AFR

AF:

0.540

Gnomad AMI

AF:

0.880

Gnomad AMR

AF:

0.868

Gnomad ASJ

AF:

0.718

Gnomad EAS

AF:

0.844

Gnomad SAS

AF:

0.520

Gnomad FIN

AF:

0.918

Gnomad MID

AF:

0.708

Gnomad NFE

AF:

0.865

Gnomad OTH

AF:

0.753

GnomAD4 exome

AF:

0.884

AC:

329

AN:

372

Hom.:

Cov.:

AF XY:

0.829

AC XY:

131

AN XY:

158

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.923

AC:

227

AN:

246

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.827

AC:

AN:

104

Other (OTH)

AF:

0.857

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.765

AC:

84946

AN:

111075

Hom.:

23764

Cov.:

AF XY:

0.760

AC XY:

25368

AN XY:

33357

show subpopulations

African (AFR)

AF:

0.540

AC:

16522

AN:

30613

American (AMR)

AF:

0.869

AC:

9204

AN:

10596

Ashkenazi Jewish (ASJ)

AF:

0.718

AC:

1885

AN:

2627

East Asian (EAS)

AF:

0.845

AC:

2928

AN:

3467

South Asian (SAS)

AF:

0.522

AC:

1381

AN:

2647

European-Finnish (FIN)

AF:

0.918

AC:

5517

AN:

6012

Middle Eastern (MID)

AF:

0.722

AC:

156

AN:

216

European-Non Finnish (NFE)

AF:

0.865

AC:

45617

AN:

52713

Other (OTH)

AF:

0.757

AC:

1141

AN:

1508

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

597

1194

1790

2387

2984

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

704

1408

2112

2816

3520

<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:

0.828

Hom.:

66423

Bravo

AF:

0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.052

(source)

PhyloP100

-1.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over