rs1555841977
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3PP5
The NM_001320643.3(LOC102724428):c.379C>T(p.Arg127Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 0)
Consequence
LOC102724428
NM_001320643.3 missense
NM_001320643.3 missense
Scores
4
1
Clinical Significance
Conservation
PhyloP100: 1.20
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.808
PP5
?
Variant 21-6116503-C-T is Pathogenic according to our data. Variant chr21-6116503-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 433140.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC102724428 | NM_001320643.3 | c.379C>T | p.Arg127Trp | missense_variant | 5/14 | ||
LOC102724428 | XM_017028208.2 | c.379C>T | p.Arg127Trp | missense_variant | 5/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes ? Cov.: 0
GnomAD3 genomes
?
Cov.:
0
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
GnomAD4 genome ? Cov.: 0
GnomAD4 genome
?
Cov.:
0
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Childhood epilepsy with centrotemporal spikes Pathogenic:1
Pathogenic, no assertion criteria provided | case-control | Bioinformatics Core, Luxembourg Center for Systems Biomedicine | Jan 01, 2017 | CAADphred>15 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_noAF
Benign
CADD
Benign
LIST_S2
Pathogenic
D
MetaRNN
Pathogenic
D
Sift4G
Pathogenic
D
Vest4
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at