1-203683316-A-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001684.5(ATP2B4):āc.111A>Gā(p.Ser37=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 1,614,012 control chromosomes in the GnomAD database, including 635,665 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.83 ( 53556 hom., cov: 32)
Exomes š: 0.89 ( 582109 hom. )
Consequence
ATP2B4
NM_001684.5 synonymous
NM_001684.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.54
Genes affected
ATP2B4 (HGNC:817): (ATPase plasma membrane Ca2+ transporting 4) The protein encoded by this gene belongs to the family of P-type primary ion transport ATPases characterized by the formation of an aspartyl phosphate intermediate during the reaction cycle. These enzymes remove bivalent calcium ions from eukaryotic cells against very large concentration gradients and play a critical role in intracellular calcium homeostasis. The mammalian plasma membrane calcium ATPase isoforms are encoded by at least four separate genes and the diversity of these enzymes is further increased by alternative splicing of transcripts. The expression of different isoforms and splice variants is regulated in a developmental, tissue- and cell type-specific manner, suggesting that these pumps are functionally adapted to the physiological needs of particular cells and tissues. This gene encodes the plasma membrane calcium ATPase isoform 4. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 1-203683316-A-G is Benign according to our data. Variant chr1-203683316-A-G is described in ClinVar as [Benign]. Clinvar id is 1598820.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.54 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2B4 | NM_001684.5 | c.111A>G | p.Ser37= | synonymous_variant | 2/21 | ENST00000357681.10 | |
ATP2B4 | NM_001001396.3 | c.111A>G | p.Ser37= | synonymous_variant | 2/22 | ||
ATP2B4 | NM_001365783.2 | c.111A>G | p.Ser37= | synonymous_variant | 2/21 | ||
ATP2B4 | NM_001365784.2 | c.111A>G | p.Ser37= | synonymous_variant | 2/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2B4 | ENST00000357681.10 | c.111A>G | p.Ser37= | synonymous_variant | 2/21 | 1 | NM_001684.5 | A1 | |
ATP2B4 | ENST00000341360.7 | c.111A>G | p.Ser37= | synonymous_variant | 2/22 | 1 | P4 | ||
ATP2B4 | ENST00000705901.1 | c.111A>G | p.Ser37= | synonymous_variant | 2/21 |
Frequencies
GnomAD3 genomes AF: 0.833 AC: 126625AN: 152042Hom.: 53548 Cov.: 32
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GnomAD3 exomes AF: 0.883 AC: 221989AN: 251452Hom.: 98670 AF XY: 0.883 AC XY: 119984AN XY: 135896
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GnomAD4 exome AF: 0.891 AC: 1302603AN: 1461852Hom.: 582109 Cov.: 61 AF XY: 0.890 AC XY: 647305AN XY: 727226
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GnomAD4 genome AF: 0.832 AC: 126668AN: 152160Hom.: 53556 Cov.: 32 AF XY: 0.831 AC XY: 61846AN XY: 74382
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at