chr17-3925408-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_174955.3(ATP2A3):āc.3102A>Gā(p.Arg1034Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 1,613,220 control chromosomes in the GnomAD database, including 104,242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: š 0.32 ( 8348 hom., cov: 31)
Exomes š: 0.36 ( 95894 hom. )
Consequence
ATP2A3
NM_174955.3 synonymous
NM_174955.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.46
Genes affected
ATP2A3 (HGNC:813): (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3) 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 calcium sequestration associated with muscular excitation and contraction. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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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=-0.58).
BP6
Variant 17-3925408-T-C is Benign according to our data. Variant chr17-3925408-T-C is described in ClinVar as [Benign]. Clinvar id is 3059152.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=1.46 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.322 AC: 48944AN: 151776Hom.: 8333 Cov.: 31
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GnomAD3 exomes AF: 0.352 AC: 87833AN: 249482Hom.: 16034 AF XY: 0.350 AC XY: 47234AN XY: 134974
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GnomAD4 exome AF: 0.360 AC: 526316AN: 1461326Hom.: 95894 Cov.: 50 AF XY: 0.358 AC XY: 260513AN XY: 726950
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GnomAD4 genome AF: 0.323 AC: 49005AN: 151894Hom.: 8348 Cov.: 31 AF XY: 0.321 AC XY: 23842AN XY: 74234
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
ATP2A3-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational 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