rs150721350
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_004320.6(ATP2A1):c.733G>A(p.Asp245Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,613,896 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. D245D) has been classified as Likely benign.
Frequency
Consequence
NM_004320.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2A1 | NM_004320.6 | c.733G>A | p.Asp245Asn | missense_variant | 8/23 | ENST00000395503.9 | |
ATP2A1 | NM_173201.5 | c.733G>A | p.Asp245Asn | missense_variant | 8/22 | ||
ATP2A1 | NM_001286075.2 | c.358G>A | p.Asp120Asn | missense_variant | 6/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A1 | ENST00000395503.9 | c.733G>A | p.Asp245Asn | missense_variant | 8/23 | 1 | NM_004320.6 | P4 | |
ATP2A1 | ENST00000357084.7 | c.733G>A | p.Asp245Asn | missense_variant | 8/22 | 2 | A1 | ||
ATP2A1 | ENST00000536376.5 | c.358G>A | p.Asp120Asn | missense_variant | 6/21 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000599 AC: 91AN: 152006Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251412Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135896
GnomAD4 exome AF: 0.0000629 AC: 92AN: 1461890Hom.: 0 Cov.: 35 AF XY: 0.0000454 AC XY: 33AN XY: 727246
GnomAD4 genome AF: 0.000599 AC: 91AN: 152006Hom.: 0 Cov.: 32 AF XY: 0.000552 AC XY: 41AN XY: 74230
ClinVar
Submissions by phenotype
Brody myopathy Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 26, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 03, 2023 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2022 | The c.733G>A (p.D245N) alteration is located in exon 8 (coding exon 8) of the ATP2A1 gene. This alteration results from a G to A substitution at nucleotide position 733, causing the aspartic acid (D) at amino acid position 245 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
ATP2A1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 03, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at