rs17629022
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002055.5(GFAP):c.461+345A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 330,546 control chromosomes in the GnomAD database, including 7,648 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 0.21 ( 3468 hom., cov: 32)
Exomes 𝑓: 0.20 ( 4180 hom. )
Consequence
GFAP
NM_002055.5 intron
NM_002055.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.58
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 Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GFAP | NM_002055.5 | c.461+345A>G | intron_variant | Intron 1 of 8 | ENST00000588735.3 | NP_002046.1 | ||
GFAP | NM_001363846.2 | c.461+345A>G | intron_variant | Intron 1 of 9 | NP_001350775.1 | |||
GFAP | NM_001242376.3 | c.461+345A>G | intron_variant | Intron 1 of 6 | NP_001229305.1 | |||
GFAP | NM_001131019.3 | c.461+345A>G | intron_variant | Intron 1 of 7 | NP_001124491.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.211 AC: 32033AN: 152012Hom.: 3464 Cov.: 32
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GnomAD4 exome AF: 0.205 AC: 36542AN: 178416Hom.: 4180 Cov.: 0 AF XY: 0.207 AC XY: 19342AN XY: 93566
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GnomAD4 genome AF: 0.211 AC: 32054AN: 152130Hom.: 3468 Cov.: 32 AF XY: 0.208 AC XY: 15439AN XY: 74378
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at