rs1553246128
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000702.4(ATP1A2):c.2841-8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,428 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_000702.4 splice_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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP1A2 | NM_000702.4 | c.2841-8C>T | splice_region_variant, intron_variant | ENST00000361216.8 | NP_000693.1 | |||
ATP1A2 | XM_047421286.1 | c.1950-8C>T | splice_region_variant, intron_variant | XP_047277242.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP1A2 | ENST00000361216.8 | c.2841-8C>T | splice_region_variant, intron_variant | 1 | NM_000702.4 | ENSP00000354490.3 | ||||
ATP1A2 | ENST00000392233.7 | c.2841-8C>T | splice_region_variant, intron_variant | 5 | ENSP00000376066.3 | |||||
ATP1A2 | ENST00000447527.1 | c.1920-8C>T | splice_region_variant, intron_variant | 2 | ENSP00000411705.1 | |||||
ATP1A2 | ENST00000463989.1 | n.177-8C>T | splice_region_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461428Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727062
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Familial hemiplegic migraine Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 20, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at