rs1499300

Positions:

• chr7-132626241-A-C
• chr7-132626241-A-G

Variant summary

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

The ENST00000378539.5(PLXNA4):​c.-87+19687T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,078 control chromosomes in the GnomAD database, including 4,216 homozygotes. 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 0.22 (4216 hom., cov: 32)
• Consequence: PLXNA4 ENST00000378539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

Genes affected

PLXNA4 (HGNC:9102): (plexin A4) Predicted to enable semaphorin receptor activity. Predicted to be involved in several processes, including axon guidance; positive regulation of axonogenesis; and regulation of GTPase activity. Predicted to act upstream of or within several processes, including nervous system development; regulation of axon extension involved in axon guidance; and regulation of negative chemotaxis. Predicted to be located in plasma membrane. Predicted to be part of semaphorin receptor complex. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLXNA4	NM_181775.4	c.-87+19687T>G		intron_variant			NP_861440.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLXNA4	ENST00000378539.5	c.-87+19687T>G		intron_variant		1		ENSP00000367800

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33046 AN: 151960 Hom.: 4198 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.218 AC: 33108 AN: 152078 Hom.: 4216 Cov.: 32 AF XY: 0.214 AC XY: 15937 AN XY: 74356

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.0868

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.224

Alfa AF: 0.170 Hom.: 4882

Bravo AF: 0.239

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.96
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1499300; hg19: chr7-132311000;