rs2289904
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001676.7(ATP12A):c.1882-95C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 1,517,908 control chromosomes in the GnomAD database, including 560 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 0.035 ( 162 hom., cov: 33)
Exomes 𝑓: 0.019 ( 398 hom. )
Consequence
ATP12A
NM_001676.7 intron
NM_001676.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.264
Genes affected
ATP12A (HGNC:13816): (ATPase H+/K+ transporting non-gastric alpha2 subunit) The protein encoded by this gene belongs to the family of P-type cation transport ATPases. This gene encodes a catalytic subunit of the ouabain-sensitive H+/K+ -ATPase that catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. It is also responsible for potassium absorption in various tissues. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]
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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=-0.8).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0806 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP12A | NM_001676.7 | c.1882-95C>T | intron_variant | ENST00000381946.5 | |||
ATP12A | NM_001185085.2 | c.1900-95C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP12A | ENST00000381946.5 | c.1882-95C>T | intron_variant | 1 | NM_001676.7 | A1 | |||
ATP12A | ENST00000218548.10 | c.1900-95C>T | intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0347 AC: 5279AN: 152204Hom.: 160 Cov.: 33
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GnomAD4 exome AF: 0.0187 AC: 25475AN: 1365586Hom.: 398 AF XY: 0.0190 AC XY: 12907AN XY: 679190
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GnomAD4 genome ? AF: 0.0347 AC: 5285AN: 152322Hom.: 162 Cov.: 33 AF XY: 0.0336 AC XY: 2505AN XY: 74500
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at