7-132450643-C-T

Variant names:

• chr7-132450643-C-T
• rs2021781
• NM_020911.2:c.1371+38649G>A

Variant summary

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

The NM_020911.2(PLXNA4):​c.1371+38649G>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 152,180 control chromosomes in the GnomAD database, including 43,424 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 (43424 hom., cov: 32)
• Consequence: PLXNA4 NM_020911.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020911.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLXNA4	NM_020911.2	MANE Select	c.1371+38649G>A		intron	N/A	NP_065962.1
	PLXNA4	NM_001393897.1		c.1371+38649G>A		intron	N/A	NP_001380826.1
	PLXNA4	NM_001105543.2		c.1371+38649G>A		intron	N/A	NP_001099013.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLXNA4	ENST00000321063.9	TSL:5 MANE Select	c.1371+38649G>A		intron	N/A	ENSP00000323194.4
	PLXNA4	ENST00000359827.7	TSL:5	c.1371+38649G>A		intron	N/A	ENSP00000352882.3
	PLXNA4	ENST00000948949.1		c.1371+38649G>A		intron	N/A	ENSP00000619008.1

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106610 AN: 152062 Hom.: 43433 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: 0.714

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.701 AC: 106604 AN: 152180 Hom.: 43424 Cov.: 32 AF XY: 0.705 AC XY: 52489 AN XY: 74400

African (AFR) AF: 0.263 AC: 10916 AN: 41500

American (AMR) AF: 0.719 AC: 10992 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2844 AN: 3472

East Asian (EAS) AF: 0.713 AC: 3675 AN: 5156

South Asian (SAS) AF: 0.805 AC: 3880 AN: 4822

European-Finnish (FIN) AF: 0.930 AC: 9868 AN: 10612

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61744 AN: 68014

Other (OTH) AF: 0.740 AC: 1562 AN: 2110

Alfa AF: 0.765 Hom.: 6136

Bravo AF: 0.665

Asia WGS AF: 0.723 AC: 2512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.92
PhyloP100		0.14
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: rs2021781; hg19: chr7-132135402;