rs186012808
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_004320.6(ATP2A1):c.2536G>A(p.Ala846Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000413 in 1,614,072 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00050 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00040 ( 3 hom. )
Consequence
ATP2A1
NM_004320.6 missense
NM_004320.6 missense
Scores
1
9
9
Clinical Significance
Conservation
PhyloP100: 4.79
Genes affected
ATP2A1 (HGNC:811): (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1) This gene encodes one of the SERCA Ca(2+)-ATPases, which are intracellular pumps located in the sarcoplasmic or endoplasmic reticula of muscle cells. This enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen, and is involved in muscular excitation and contraction. Mutations in this gene cause some autosomal recessive forms of Brody disease, characterized by increasing impairment of muscular relaxation during exercise. Alternative splicing results in three transcript variants encoding different isoforms. [provided by RefSeq, Oct 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0117560625).
BP6
Variant 16-28902591-G-A is Benign according to our data. Variant chr16-28902591-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 431853.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1, Benign=2}.
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000404 (590/1461846) while in subpopulation AFR AF= 0.00108 (36/33480). AF 95% confidence interval is 0.000798. There are 3 homozygotes in gnomad4_exome. There are 314 alleles in male gnomad4_exome subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP2A1 | NM_004320.6 | c.2536G>A | p.Ala846Thr | missense_variant | 18/23 | ENST00000395503.9 | NP_004311.1 | |
ATP2A1 | NM_173201.5 | c.2536G>A | p.Ala846Thr | missense_variant | 18/22 | NP_775293.1 | ||
ATP2A1 | NM_001286075.2 | c.2161G>A | p.Ala721Thr | missense_variant | 16/21 | NP_001273004.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP2A1 | ENST00000395503.9 | c.2536G>A | p.Ala846Thr | missense_variant | 18/23 | 1 | NM_004320.6 | ENSP00000378879.5 | ||
ATP2A1 | ENST00000357084.7 | c.2536G>A | p.Ala846Thr | missense_variant | 18/22 | 2 | ENSP00000349595.3 | |||
ATP2A1 | ENST00000536376.5 | c.2161G>A | p.Ala721Thr | missense_variant | 16/21 | 2 | ENSP00000443101.1 |
Frequencies
GnomAD3 genomes AF: 0.000500 AC: 76AN: 152108Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000729 AC: 183AN: 251164Hom.: 2 AF XY: 0.000685 AC XY: 93AN XY: 135786
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GnomAD4 exome AF: 0.000404 AC: 590AN: 1461846Hom.: 3 Cov.: 34 AF XY: 0.000432 AC XY: 314AN XY: 727232
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GnomAD4 genome AF: 0.000499 AC: 76AN: 152226Hom.: 0 Cov.: 31 AF XY: 0.000470 AC XY: 35AN XY: 74436
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:3
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Brody myopathy Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 26, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 15, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 04, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
D;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Uncertain
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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