rs281877

Positions:

• chr7-132136709-T-A

Variant summary

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

The NM_020911.2(PLXNA4):​c.5439-3510A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,086 control chromosomes in the GnomAD database, including 6,291 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 0.25 (6291 hom., cov: 32)
• Consequence: PLXNA4 NM_020911.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLXNA4	NM_020911.2	c.5439-3510A>T		intron_variant		ENST00000321063.9	NP_065962.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLXNA4	ENST00000321063.9	c.5439-3510A>T		intron_variant		5	NM_020911.2	ENSP00000323194.4
PLXNA4	ENST00000359827.7	c.5439-3510A>T		intron_variant		5		ENSP00000352882.3

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37835 AN: 151968 Hom.: 6283 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.249 AC: 37883 AN: 152086 Hom.: 6291 Cov.: 32 AF XY: 0.248 AC XY: 18460 AN XY: 74360

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.0786

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.231

Alfa AF: 0.212 Hom.: 592

Bravo AF: 0.271

Asia WGS AF: 0.286 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs281877; hg19: chr7-131821468;