chr19-41966970-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_152296.5(ATP1A3):c.3014-5T>C 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 0.00000387 in 1,551,394 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_152296.5 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 |
---|---|---|---|---|---|---|---|
ATP1A3 | NM_152296.5 | c.3014-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000648268.1 | |||
ATP1A3 | NM_001256213.2 | c.3047-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
ATP1A3 | NM_001256214.2 | c.3053-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
ATP1A3 | XM_047438862.1 | c.2924-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A3 | ENST00000648268.1 | c.3014-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_152296.5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151984Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000357 AC: 5AN: 1399410Hom.: 0 Cov.: 36 AF XY: 0.00000435 AC XY: 3AN XY: 690214
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151984Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74244
ClinVar
Submissions by phenotype
Dystonia 12 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 26, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at