rs2301573

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015103.3(PLXND1):​c.1489-357A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0945 in 152,158 control chromosomes in the GnomAD database, including 902 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 0.095 ( 902 hom., cov: 33)

Consequence

PLXND1
NM_015103.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.311
Variant links:
Genes affected
PLXND1 (HGNC:9107): (plexin D1) Enables protein domain specific binding activity. Predicted to be involved in several processes, including endothelial cell migration; nervous system development; and regulation of angiogenesis. Predicted to act upstream of or within several processes, including circulatory system development; dichotomous subdivision of terminal units involved in salivary gland branching; and positive regulation of protein binding activity. Located in lamellipodium. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PLXND1NM_015103.3 linkuse as main transcriptc.1489-357A>G intron_variant ENST00000324093.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PLXND1ENST00000324093.9 linkuse as main transcriptc.1489-357A>G intron_variant 1 NM_015103.3 P1Q9Y4D7-1
PLXND1ENST00000505237.2 linkuse as main transcriptc.178-357A>G intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0945
AC:
14364
AN:
152040
Hom.:
896
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0541
Gnomad AMI
AF:
0.103
Gnomad AMR
AF:
0.163
Gnomad ASJ
AF:
0.0881
Gnomad EAS
AF:
0.256
Gnomad SAS
AF:
0.166
Gnomad FIN
AF:
0.0765
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.0894
Gnomad OTH
AF:
0.0928
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0945
AC:
14380
AN:
152158
Hom.:
902
Cov.:
33
AF XY:
0.0998
AC XY:
7424
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.0542
Gnomad4 AMR
AF:
0.163
Gnomad4 ASJ
AF:
0.0881
Gnomad4 EAS
AF:
0.257
Gnomad4 SAS
AF:
0.166
Gnomad4 FIN
AF:
0.0765
Gnomad4 NFE
AF:
0.0894
Gnomad4 OTH
AF:
0.0914
Alfa
AF:
0.0793
Hom.:
98
Bravo
AF:
0.0962
Asia WGS
AF:
0.182
AC:
633
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
3.0
DANN
Benign
0.67

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2301573; hg19: chr3-129305919; API