rs2269414
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001001344.3(ATP2B3):c.2326+20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0835 in 1,185,148 control chromosomes in the GnomAD database, including 4,718 homozygotes. There are 32,347 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.15 ( 1577 hom., 4487 hem., cov: 23)
Exomes 𝑓: 0.077 ( 3141 hom. 27860 hem. )
Consequence
ATP2B3
NM_001001344.3 intron
NM_001001344.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.10
Genes affected
ATP2B3 (HGNC:816): (ATPase plasma membrane Ca2+ transporting 3) 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 3. 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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant X-153556438-C-T is Benign according to our data. Variant chrX-153556438-C-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2B3 | NM_001001344.3 | c.2326+20C>T | intron_variant | ENST00000263519.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2B3 | ENST00000263519.5 | c.2326+20C>T | intron_variant | 1 | NM_001001344.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.148 AC: 16382AN: 110838Hom.: 1575 Cov.: 23 AF XY: 0.135 AC XY: 4479AN XY: 33106
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GnomAD3 exomes AF: 0.0963 AC: 13763AN: 142899Hom.: 819 AF XY: 0.0959 AC XY: 4134AN XY: 43113
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GnomAD4 exome AF: 0.0769 AC: 82619AN: 1074258Hom.: 3141 Cov.: 32 AF XY: 0.0802 AC XY: 27860AN XY: 347176
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GnomAD4 genome AF: 0.148 AC: 16394AN: 110890Hom.: 1577 Cov.: 23 AF XY: 0.135 AC XY: 4487AN XY: 33168
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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