rs3744470
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002055.5(GFAP):c.*814T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,462 control chromosomes in the GnomAD database, including 1,229 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.12 ( 1226 hom., cov: 32)
Exomes 𝑓: 0.097 ( 3 hom. )
Consequence
GFAP
NM_002055.5 3_prime_UTR
NM_002055.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.190
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 17-44906533-A-T is Benign according to our data. Variant chr17-44906533-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 323601.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GFAP | NM_002055.5 | c.*814T>A | 3_prime_UTR_variant | 9/9 | ENST00000588735.3 | ||
GFAP | NM_001363846.2 | c.*814T>A | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GFAP | ENST00000588735.3 | c.*814T>A | 3_prime_UTR_variant | 9/9 | 1 | NM_002055.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.122 AC: 18583AN: 151964Hom.: 1225 Cov.: 32
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GnomAD4 exome AF: 0.0974 AC: 37AN: 380Hom.: 3 Cov.: 0 AF XY: 0.0938 AC XY: 18AN XY: 192
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GnomAD4 genome ? AF: 0.122 AC: 18599AN: 152082Hom.: 1226 Cov.: 32 AF XY: 0.125 AC XY: 9283AN XY: 74356
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Name
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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