rs3747626
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_ModerateBS2
The NM_000702.4(ATP1A2):c.2563+4C>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000702.4 splice_donor_region, 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 |
---|---|---|---|---|---|---|---|
ATP1A2 | NM_000702.4 | c.2563+4C>A | splice_donor_region_variant, intron_variant | ENST00000361216.8 | |||
ATP1A2 | XM_047421286.1 | c.1672+4C>A | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A2 | ENST00000361216.8 | c.2563+4C>A | splice_donor_region_variant, intron_variant | 1 | NM_000702.4 | P1 | |||
ATP1A2 | ENST00000392233.7 | c.2563+4C>A | splice_donor_region_variant, intron_variant | 5 | |||||
ATP1A2 | ENST00000447527.1 | c.1695+4C>A | splice_donor_region_variant, intron_variant | 2 | |||||
ATP1A2 | ENST00000472488.5 | n.2666+4C>A | splice_donor_region_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250812Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135708
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461664Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 727130
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at