chr16-28898301-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_004320.6(ATP2A1):c.1614G>A(p.Thr538=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0095 in 1,614,238 control chromosomes in the GnomAD database, including 476 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T538T) has been classified as Likely benign.
Frequency
Consequence
NM_004320.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2A1 | NM_004320.6 | c.1614G>A | p.Thr538= | synonymous_variant | 14/23 | ENST00000395503.9 | |
ATP2A1 | NM_173201.5 | c.1614G>A | p.Thr538= | synonymous_variant | 14/22 | ||
ATP2A1 | NM_001286075.2 | c.1239G>A | p.Thr413= | synonymous_variant | 12/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A1 | ENST00000395503.9 | c.1614G>A | p.Thr538= | synonymous_variant | 14/23 | 1 | NM_004320.6 | P4 | |
ATP2A1 | ENST00000357084.7 | c.1614G>A | p.Thr538= | synonymous_variant | 14/22 | 2 | A1 | ||
ATP2A1 | ENST00000536376.5 | c.1239G>A | p.Thr413= | synonymous_variant | 12/21 | 2 | |||
ATP2A1 | ENST00000564732.1 | c.*257G>A | 3_prime_UTR_variant, NMD_transcript_variant | 6/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0162 AC: 2460AN: 152236Hom.: 69 Cov.: 32
GnomAD3 exomes AF: 0.0186 AC: 4673AN: 251334Hom.: 246 AF XY: 0.0169 AC XY: 2298AN XY: 135898
GnomAD4 exome AF: 0.00881 AC: 12883AN: 1461884Hom.: 407 Cov.: 32 AF XY: 0.00861 AC XY: 6263AN XY: 727242
GnomAD4 genome AF: 0.0161 AC: 2454AN: 152354Hom.: 69 Cov.: 32 AF XY: 0.0168 AC XY: 1251AN XY: 74498
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 15, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 01, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Brody myopathy Benign:2
Benign, 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at