rs11107437

chr12-94203667-C-G

Variant summary

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

The NM_005761.3(PLXNC1):c.1440-5923C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0975 in 152,246 control chromosomes in the GnomAD database, including 845 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 0.097 (845 hom., cov: 32)
• Consequence: PLXNC1 NM_005761.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

Genes affected

PLXNC1 (HGNC:9106): (plexin C1) This gene encodes a member of the plexin family. Plexins are transmembrane receptors for semaphorins, a large family of proteins that regulate axon guidance, cell motility and migration, and the immune response. The encoded protein and its ligand regulate melanocyte adhesion, and viral semaphorins may modulate the immune response by binding to this receptor. The encoded protein may be a tumor suppressor protein for melanoma. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jan 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLXNC1	NM_005761.3	c.1440-5923C>G		intron_variant		ENST00000258526.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLXNC1	ENST00000258526.9	c.1440-5923C>G		intron_variant		1	NM_005761.3	P1
PLXNC1	ENST00000551850.1	c.288-5923C>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0975 AC: 14839 AN: 152128 Hom.: 844 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0946

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0854

Gnomad OTH AF: 0.0938

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

GnomAD4 genome AF: 0.0975 AC: 14842 AN: 152246 Hom.: 845 Cov.: 32 AF XY: 0.0973 AC XY: 7244 AN XY: 74440

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0946

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0458

Gnomad4 NFE AF: 0.0854

Gnomad4 OTH AF: 0.0928

Alfa AF: 0.0842 Hom.: 70

Bravo AF: 0.102

Asia WGS AF: 0.162 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.80
Dann	Benign	0.31

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: rs11107437; hg19: chr12-94597443;