chr13-112819312-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_015205.3(ATP11A):c.579C>T(p.Tyr193=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000979 in 1,614,188 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000095 ( 0 hom. )
Consequence
ATP11A
NM_015205.3 synonymous
NM_015205.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.566
Genes affected
ATP11A (HGNC:13552): (ATPase phospholipid transporting 11A) The protein encoded by this gene is an integral membrane ATPase. The encoded protein is probably phosphorylated in its intermediate state and likely drives the transport of ions such as calcium across membranes. [provided by RefSeq, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 13-112819312-C-T is Benign according to our data. Variant chr13-112819312-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 749843.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.566 with no splicing effect.
BS2
High AC in GnomAd4 at 19 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP11A | NM_015205.3 | c.579C>T | p.Tyr193= | synonymous_variant | 7/30 | ENST00000375645.8 | NP_056020.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP11A | ENST00000375645.8 | c.579C>T | p.Tyr193= | synonymous_variant | 7/30 | 5 | NM_015205.3 | ENSP00000364796 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152230Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000163 AC: 41AN: 251264Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135782
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GnomAD4 exome AF: 0.0000951 AC: 139AN: 1461840Hom.: 0 Cov.: 31 AF XY: 0.0000894 AC XY: 65AN XY: 727208
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GnomAD4 genome AF: 0.000125 AC: 19AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74500
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 17, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
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