rs6950129

Variant names:

• chr7-132280708-A-G
• rs6950129
• NM_020911.2:c.1503+17383T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020911.2(PLXNA4):​c.1503+17383T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0882 in 152,102 control chromosomes in the GnomAD database, including 763 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 0.088 (763 hom., cov: 32)
• Consequence: PLXNA4 NM_020911.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLXNA4	NM_020911.2	c.1503+17383T>C		intron_variant	Intron 4 of 31	ENST00000321063.9	NP_065962.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLXNA4	ENST00000321063.9	c.1503+17383T>C		intron_variant	Intron 4 of 31	5	NM_020911.2	ENSP00000323194.4
PLXNA4	ENST00000359827.7	c.1503+17383T>C		intron_variant	Intron 4 of 31	5		ENSP00000352882.3

Frequencies

GnomAD3 genomes AF: 0.0881 AC: 13390 AN: 151984 Hom.: 757 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0555

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0330

Gnomad FIN AF: 0.0295

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0760

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.0882 AC: 13417 AN: 152102 Hom.: 763 Cov.: 32 AF XY: 0.0837 AC XY: 6223 AN XY: 74386

African (AFR) AF: 0.155 AC: 6422 AN: 41472

American (AMR) AF: 0.0553 AC: 845 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0631 AC: 219 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5166

South Asian (SAS) AF: 0.0330 AC: 159 AN: 4820

European-Finnish (FIN) AF: 0.0295 AC: 313 AN: 10622

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0760 AC: 5165 AN: 67970

Other (OTH) AF: 0.0849 AC: 179 AN: 2108

Alfa AF: 0.103 Hom.: 354

Bravo AF: 0.0935

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.10
DANN	Benign	0.52
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6950129; hg19: chr7-131965467;