chr19-41966865-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_152296.5(ATP1A3):c.*72A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000686 in 1,546,304 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00014 ( 1 hom., cov: 29)
Exomes 𝑓: 0.000061 ( 0 hom. )
Consequence
ATP1A3
NM_152296.5 3_prime_UTR
NM_152296.5 3_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: -0.0370
Genes affected
ATP1A3 (HGNC:801): (ATPase Na+/K+ transporting subunit alpha 3) 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 3 subunit. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
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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=-0.51).
BP6
?
Variant 19-41966865-T-C is Benign according to our data. Variant chr19-41966865-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1190789.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00014 (21/150338) while in subpopulation AMR AF= 0.000795 (12/15090). AF 95% confidence interval is 0.000459. There are 1 homozygotes in gnomad4. There are 14 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
?
High AC in GnomAd at 20 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1A3 | NM_152296.5 | c.*72A>G | 3_prime_UTR_variant | 23/23 | ENST00000648268.1 | ||
ATP1A3 | NM_001256213.2 | c.*72A>G | 3_prime_UTR_variant | 23/23 | |||
ATP1A3 | NM_001256214.2 | c.*72A>G | 3_prime_UTR_variant | 23/23 | |||
ATP1A3 | XM_047438862.1 | c.*72A>G | 3_prime_UTR_variant | 23/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A3 | ENST00000648268.1 | c.*72A>G | 3_prime_UTR_variant | 23/23 | NM_152296.5 |
Frequencies
GnomAD3 genomes ? AF: 0.000133 AC: 20AN: 150224Hom.: 1 Cov.: 29
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GnomAD3 exomes AF: 0.000218 AC: 33AN: 151366Hom.: 0 AF XY: 0.000212 AC XY: 17AN XY: 80134
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GnomAD4 exome AF: 0.0000609 AC: 85AN: 1395966Hom.: 0 Cov.: 34 AF XY: 0.0000712 AC XY: 49AN XY: 688550
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GnomAD4 genome ? AF: 0.000140 AC: 21AN: 150338Hom.: 1 Cov.: 29 AF XY: 0.000191 AC XY: 14AN XY: 73326
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 23, 2020 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
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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