rs2341823

chr7-132409104-T-G

Variant summary

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

The NM_020911.2(PLXNA4):c.1371+80188A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,154 control chromosomes in the GnomAD database, including 12,414 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 0.29 (12414 hom., cov: 32)
• Consequence: PLXNA4 NM_020911.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

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]

LOC105375511 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLXNA4	NM_020911.2	c.1371+80188A>C		intron_variant		ENST00000321063.9
LOC105375511	XR_927983.3	n.198-521T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLXNA4	ENST00000321063.9	c.1371+80188A>C		intron_variant		5	NM_020911.2	P1
PLXNA4	ENST00000359827.7	c.1371+80188A>C		intron_variant		5		P1
PLXNA4	ENST00000423507.6	c.1372-23809A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43249 AN: 152036 Hom.: 12360 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0729

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.285 AC: 43370 AN: 152154 Hom.: 12414 Cov.: 32 AF XY: 0.280 AC XY: 20869 AN XY: 74404

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.0322

Gnomad4 NFE AF: 0.0729

Gnomad4 OTH AF: 0.234

Alfa AF: 0.192 Hom.: 891

Bravo AF: 0.324

Asia WGS AF: 0.284 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.7
Dann	Benign	0.43

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: rs2341823; hg19: chr7-132093863;