chr7-132643211-C-T

Variant names:

• chr7-132643211-C-T
• rs11773117
• ENST00000378539.5:c.-87+2717G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PLXNA4	NM_181775.4	c.-87+2717G>A		intron_variant	Intron 2 of 4		NP_861440.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLXNA4	ENST00000378539.5	c.-87+2717G>A		intron_variant	Intron 2 of 4	1		ENSP00000367800.5

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

African (AFR) AF: 0.0276 AC: 1145 AN: 41540

American (AMR) AF: 0.0691 AC: 1057 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3472

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.0330 AC: 159 AN: 4822

European-Finnish (FIN) AF: 0.116 AC: 1232 AN: 10594

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8953 AN: 67980

Other (OTH) AF: 0.0858 AC: 181 AN: 2110

Alfa AF: 0.118 Hom.: 636

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
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11773117; hg19: chr7-132327970;