rs757455246
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004320.6(ATP2A1):c.1765-4C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,558,756 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004320.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2A1 | NM_004320.6 | c.1765-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000395503.9 | |||
ATP2A1 | NM_001286075.2 | c.1390-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
ATP2A1 | NM_173201.5 | c.1765-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A1 | ENST00000395503.9 | c.1765-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004320.6 | P4 | |||
ATP2A1 | ENST00000357084.7 | c.1765-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | A1 | ||||
ATP2A1 | ENST00000536376.5 | c.1390-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
ATP2A1 | ENST00000564732.1 | c.*408-4C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000953 AC: 2AN: 209946Hom.: 0 AF XY: 0.00000902 AC XY: 1AN XY: 110882
GnomAD4 exome AF: 0.0000405 AC: 57AN: 1406702Hom.: 0 Cov.: 32 AF XY: 0.0000477 AC XY: 33AN XY: 691858
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74256
ClinVar
Submissions by phenotype
Brody myopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 19, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at