chr7-100310486-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001004351.5(SPDYE3):c.452C>T(p.Ala151Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 5)
Exomes 𝑓: 0.000016 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SPDYE3
NM_001004351.5 missense
NM_001004351.5 missense
Scores
18
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.748
Genes affected
SPDYE3 (HGNC:35462): (speedy/RINGO cell cycle regulator family member E3) Predicted to enable protein kinase binding activity. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.049823344).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPDYE3 | NM_001004351.5 | c.452C>T | p.Ala151Val | missense_variant | 3/11 | ENST00000332397.6 | |
SPDYE3 | XM_047420404.1 | c.452C>T | p.Ala151Val | missense_variant | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPDYE3 | ENST00000332397.6 | c.452C>T | p.Ala151Val | missense_variant | 3/11 | 1 | NM_001004351.5 | P1 | |
ENST00000685724.2 | n.751-9763G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 18406Hom.: 0 Cov.: 5 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000161 AC: 6AN: 372286Hom.: 0 Cov.: 0 AF XY: 0.0000152 AC XY: 3AN XY: 196794
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GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 18406Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0AN XY: 7948
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N;N
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MutPred
Loss of disorder (P = 0.1364);
MVP
MPC
ClinPred
T
GERP RS
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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