chr7-132643211-C-T

Position:

• chr7-132643211-C-T

Variant summary

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

The ENST00000378539.5(PLXNA4):​c.-87+2717G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0875 in 152,182 control chromosomes in the GnomAD database, including 783 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 0.087 (783 hom., cov: 31)
• Consequence: PLXNA4 ENST00000378539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLXNA4	NM_181775.4	c.-87+2717G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLXNA4	ENST00000378539.5	c.-87+2717G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0876 AC: 13314 AN: 152064 Hom.: 783 Cov.: 31

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0692

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.0875 AC: 13310 AN: 152182 Hom.: 783 Cov.: 31 AF XY: 0.0835 AC XY: 6214 AN XY: 74388

Gnomad4 AFR AF: 0.0276

Gnomad4 AMR AF: 0.0691

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0330

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.0858

Alfa AF: 0.117 Hom.: 571

Bravo AF: 0.0812

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.6
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11773117; hg19: chr7-132327970;