chr1-116374023-CT-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_000701.8(ATP1A1):c.12+501del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.92 ( 64302 hom., cov: 0)
Exomes 𝑓: 0.89 ( 498262 hom. )
Consequence
ATP1A1
NM_000701.8 intron
NM_000701.8 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00
Genes affected
ATP1A1 (HGNC:799): (ATPase Na+/K+ transporting subunit alpha 1) The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of Na+/K+ -ATPases. Na+/K+ -ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na and K ions across the plasma membrane. These gradients are essential for osmoregulation, for sodium-coupled transport of a variety of organic and inorganic molecules, and for electrical excitability of nerve and muscle. This enzyme is composed of two subunits, a large catalytic subunit (alpha) and a smaller glycoprotein subunit (beta). The catalytic subunit of Na+/K+ -ATPase is encoded by multiple genes. This gene encodes an alpha 1 subunit. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 1-116374023-CT-C is Benign according to our data. Variant chr1-116374023-CT-C is described in ClinVar as [Benign]. Clinvar id is 1280079.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1A1 | NM_000701.8 | c.12+501del | intron_variant | ENST00000295598.10 | |||
ATP1A1 | NM_001160233.2 | c.-206del | 5_prime_UTR_variant | 1/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A1 | ENST00000295598.10 | c.12+501del | intron_variant | 1 | NM_000701.8 | P4 | |||
ATP1A1 | ENST00000537345.5 | c.-206del | 5_prime_UTR_variant | 1/23 | 2 | A1 | |||
ATP1A1 | ENST00000418797.5 | c.-82+1103del | intron_variant | 3 | |||||
ATP1A1 | ENST00000488733.1 | n.255+501del | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.918 AC: 139642AN: 152072Hom.: 64247 Cov.: 0
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GnomAD4 exome AF: 0.890 AC: 1118553AN: 1257048Hom.: 498262 Cov.: 0 AF XY: 0.890 AC XY: 541927AN XY: 608910
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GnomAD4 genome ? AF: 0.918 AC: 139754AN: 152188Hom.: 64302 Cov.: 0 AF XY: 0.921 AC XY: 68486AN XY: 74396
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 10, 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