dbSNP rs865569: PLXNC1:c.3087+31T>C (chr12-94255327-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_005761.3(PLXNC1):c.3087+31T>C variant causes a intron change. The variant allele was found at a frequency of 0.821 in 1,397,062 control chromosomes in the GnomAD database, including 473,782 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 0.78 ( 46709 hom., cov: 34)

Exomes 𝑓: 0.83 ( 427073 hom. )

Consequence

PLXNC1
NM_005761.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.58

Publications

17 publications found

Variant links:

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]

PLXNC1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.22).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLXNC1	NM_005761.3 link	c.3087+31T>C		intron_variant	Intron 17 of 30	ENST00000258526.9	NP_005752.1	O60486

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLXNC1	ENST00000258526.9 link	c.3087+31T>C		intron_variant	Intron 17 of 30	1	NM_005761.3	ENSP00000258526.4		O60486

Frequencies

GnomAD3 genomes

AF:

0.778

AC:

118368

AN:

152120

Hom.:

46694

Cov.:

show subpopulations

Gnomad AFR

AF:

0.659

Gnomad AMI

AF:

0.889

Gnomad AMR

AF:

0.776

Gnomad ASJ

AF:

0.820

Gnomad EAS

AF:

0.617

Gnomad SAS

AF:

0.772

Gnomad FIN

AF:

0.880

Gnomad MID

AF:

0.769

Gnomad NFE

AF:

0.844

Gnomad OTH

AF:

0.782

GnomAD2 exomes

AF:

0.796

AC:

198874

AN:

249868

AF XY:

0.801

show subpopulations

Gnomad AFR exome

AF:

0.660

Gnomad AMR exome

AF:

0.747

Gnomad ASJ exome

AF:

0.816

Gnomad EAS exome

AF:

0.615

Gnomad FIN exome

AF:

0.880

Gnomad NFE exome

AF:

0.844

Gnomad OTH exome

AF:

0.811

GnomAD4 exome

AF:

0.826

AC:

1028519

AN:

1244824

Hom.:

427073

Cov.:

AF XY:

0.826

AC XY:

520714

AN XY:

630640

show subpopulations

African (AFR)

AF:

0.655

AC:

19187

AN:

29284

American (AMR)

AF:

0.752

AC:

33439

AN:

44446

Ashkenazi Jewish (ASJ)

AF:

0.817

AC:

20275

AN:

24820

East Asian (EAS)

AF:

0.632

AC:

24443

AN:

38686

South Asian (SAS)

AF:

0.787

AC:

64462

AN:

81864

European-Finnish (FIN)

AF:

0.884

AC:

47068

AN:

53234

Middle Eastern (MID)

AF:

0.802

AC:

4313

AN:

5376

European-Non Finnish (NFE)

AF:

0.845

AC:

772457

AN:

914052

Other (OTH)

AF:

0.808

AC:

42875

AN:

53062

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

8922

17844

26766

35688

44610

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15934

31868

47802

63736

79670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.778

AC:

118427

AN:

152238

Hom.:

46709

Cov.:

AF XY:

0.777

AC XY:

57842

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.659

AC:

27355

AN:

41502

American (AMR)

AF:

0.776

AC:

11873

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.820

AC:

2845

AN:

3470

East Asian (EAS)

AF:

0.617

AC:

3194

AN:

5180

South Asian (SAS)

AF:

0.772

AC:

3728

AN:

4830

European-Finnish (FIN)

AF:

0.880

AC:

9334

AN:

10610

Middle Eastern (MID)

AF:

0.759

AC:

223

AN:

294

European-Non Finnish (NFE)

AF:

0.844

AC:

57423

AN:

68026

Other (OTH)

AF:

0.777

AC:

1641

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1308

2616

3923

5231

6539

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

864

1728

2592

3456

4320

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.819

Hom.:

97532

Bravo

AF:

0.763

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.22

CADD

Benign

(source)

DANN

Benign

0.77

PhyloP100

4.6

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over