rs2021782

Positions:

• chr7-132450236-C-T

Variant summary

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

The NM_020911.2(PLXNA4):​c.1371+39056G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,104 control chromosomes in the GnomAD database, including 43,402 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 0.70 (43402 hom., cov: 32)
• Consequence: PLXNA4 NM_020911.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLXNA4	NM_020911.2	c.1371+39056G>A		intron_variant		ENST00000321063.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLXNA4	ENST00000321063.9	c.1371+39056G>A		intron_variant		5	NM_020911.2	P1
PLXNA4	ENST00000359827.7	c.1371+39056G>A		intron_variant		5		P1
PLXNA4	ENST00000423507.6	c.1371+39056G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106566 AN: 151986 Hom.: 43411 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.701 AC: 106560 AN: 152104 Hom.: 43402 Cov.: 32 AF XY: 0.706 AC XY: 52464 AN XY: 74356

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.930

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.740

Alfa AF: 0.775 Hom.: 5512

Bravo AF: 0.665

Asia WGS AF: 0.722 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.063
DANN	Benign	0.35

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: rs2021782; hg19: chr7-132134995;