rs5945431

chrX-154473373-G-AchrX-154473373-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLXNA3	NM_017514.5	c.*688G>A		3_prime_UTR_variant	33/33	ENST00000369682.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLXNA3	ENST00000369682.4	c.*688G>A		3_prime_UTR_variant	33/33	1	NM_017514.5	P1

Frequencies

GnomAD3 genomes AF: 0.765 AC: 84912 AN: 111021 Hom.: 23763 Cov.: 24 AF XY: 0.761 AC XY: 25331 AN XY: 33293

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.: 93 Cov.: 0 AF XY: 0.829 AC XY: 131 AN XY: 158

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.923

Gnomad4 NFE exome AF: 0.827

Gnomad4 OTH exome AF: 0.857

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.765 AC: 84946 AN: 111075 Hom.: 23764 Cov.: 24 AF XY: 0.760 AC XY: 25368 AN XY: 33357

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.757

Alfa AF: 0.838 Hom.: 51727

Bravo AF: 0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.052
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

LitVar

Other links and lift over

dbSNP: rs5945431; hg19: chrX-153701716;