rs267607509
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_002055.5(GFAP):āc.382G>Cā(p.Asp128His) variant causes a missense change. The variant allele was found at a frequency of 0.0000089 in 1,461,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.0000089 ( 0 hom. )
Consequence
GFAP
NM_002055.5 missense
NM_002055.5 missense
Scores
8
9
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.01
Genes affected
GFAP (HGNC:4235): (glial fibrillary acidic protein) This gene encodes one of the major intermediate filament proteins of mature astrocytes. It is used as a marker to distinguish astrocytes from other glial cells during development. Mutations in this gene cause Alexander disease, a rare disorder of astrocytes in the central nervous system. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.948
BS2
High AC in GnomAdExome4 at 13 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GFAP | NM_002055.5 | c.382G>C | p.Asp128His | missense_variant | Exon 1 of 9 | ENST00000588735.3 | NP_002046.1 | |
| GFAP | NM_001363846.2 | c.382G>C | p.Asp128His | missense_variant | Exon 1 of 10 | NP_001350775.1 | ||
| GFAP | NM_001242376.3 | c.382G>C | p.Asp128His | missense_variant | Exon 1 of 7 | NP_001229305.1 | ||
| GFAP | NM_001131019.3 | c.382G>C | p.Asp128His | missense_variant | Exon 1 of 8 | NP_001124491.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461004Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726882
GnomAD4 exome
AF:
AC:
13
AN:
1461004
Hom.:
Cov.:
31
AF XY:
AC XY:
7
AN XY:
726882
Gnomad4 AFR exome
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Gnomad4 AMR exome
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Gnomad4 ASJ exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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Gnomad4 FIN exome
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Gnomad4 NFE exome
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Gnomad4 OTH exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Pathogenic
.;D;.;.;.;.;D;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T;D;T;T;D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
.;M;.;.;M;M;.;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Uncertain
.;.;D;.;D;.;.;.;.;.
REVEL
Pathogenic
Sift
Uncertain
.;.;D;.;D;.;.;.;.;.
Sift4G
Uncertain
.;.;D;.;T;.;D;T;.;.
Polyphen
1.0
.;D;.;.;.;.;.;.;.;.
Vest4
0.28, 0.72, 0.33
MutPred
Gain of MoRF binding (P = 0.0452);Gain of MoRF binding (P = 0.0452);Gain of MoRF binding (P = 0.0452);.;Gain of MoRF binding (P = 0.0452);Gain of MoRF binding (P = 0.0452);Gain of MoRF binding (P = 0.0452);Gain of MoRF binding (P = 0.0452);Gain of MoRF binding (P = 0.0452);Gain of MoRF binding (P = 0.0452);
MVP
1.0
MPC
1.3
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.