rs10508606
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032812.9(PLXDC2):c.113-14573T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0527 in 152,308 control chromosomes in the GnomAD database, including 275 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 0.053 ( 275 hom., cov: 32)
Consequence
PLXDC2
NM_032812.9 intron
NM_032812.9 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.238
Genes affected
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0752 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLXDC2 | NM_032812.9 | c.113-14573T>G | intron_variant | ENST00000377252.5 | |||
PLXDC2 | NM_001282736.2 | c.113-14573T>G | intron_variant | ||||
PLXDC2 | XM_011519750.3 | c.113-14573T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLXDC2 | ENST00000377252.5 | c.113-14573T>G | intron_variant | 1 | NM_032812.9 | P1 | |||
PLXDC2 | ENST00000377242.7 | c.113-14573T>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0528 AC: 8031AN: 152190Hom.: 275 Cov.: 32
GnomAD3 genomes
?
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8031
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152190
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0527 AC: 8026AN: 152308Hom.: 275 Cov.: 32 AF XY: 0.0501 AC XY: 3735AN XY: 74484
GnomAD4 genome
?
AF:
AC:
8026
AN:
152308
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32
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3735
AN XY:
74484
Gnomad4 AFR
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60
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at