chr9-128617719-C-A
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001130438.3(SPTAN1):c.5437C>A(p.Arg1813=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0182 in 1,614,074 control chromosomes in the GnomAD database, including 447 homozygotes. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. R1813R) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.017 ( 34 hom., cov: 32)
Exomes 𝑓: 0.018 ( 413 hom. )
Consequence
SPTAN1
NM_001130438.3 synonymous
NM_001130438.3 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 3.99
Genes affected
SPTAN1 (HGNC:11273): (spectrin alpha, non-erythrocytic 1) Spectrins are a family of filamentous cytoskeletal proteins that function as essential scaffold proteins that stabilize the plasma membrane and organize intracellular organelles. Spectrins are composed of alpha and beta dimers that associate to form tetramers linked in a head-to-head arrangement. This gene encodes an alpha spectrin that is specifically expressed in nonerythrocytic cells. The encoded protein has been implicated in other cellular functions including DNA repair and cell cycle regulation. Mutations in this gene are the cause of early infantile epileptic encephalopathy-5. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 9-128617719-C-A is Benign according to our data. Variant chr9-128617719-C-A is described in ClinVar as [Benign]. Clinvar id is 160017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128617719-C-A is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0741 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTAN1 | NM_001130438.3 | c.5437C>A | p.Arg1813= | synonymous_variant | 42/57 | ENST00000372739.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTAN1 | ENST00000372739.7 | c.5437C>A | p.Arg1813= | synonymous_variant | 42/57 | 1 | NM_001130438.3 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0170 AC: 2588AN: 152132Hom.: 34 Cov.: 32
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GnomAD3 exomes AF: 0.0247 AC: 6195AN: 251294Hom.: 132 AF XY: 0.0233 AC XY: 3170AN XY: 135844
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GnomAD4 exome AF: 0.0183 AC: 26752AN: 1461824Hom.: 413 Cov.: 39 AF XY: 0.0183 AC XY: 13331AN XY: 727218
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GnomAD4 genome AF: 0.0170 AC: 2592AN: 152250Hom.: 34 Cov.: 32 AF XY: 0.0177 AC XY: 1319AN XY: 74452
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ClinVar
Significance: Benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 04, 2018 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 05, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Developmental and epileptic encephalopathy, 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at