rs201215311
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_000702.4(ATP1A2):c.2742G>A(p.Thr914=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,614,146 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T914T) has been classified as Likely benign.
Frequency
Consequence
NM_000702.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP1A2 | NM_000702.4 | c.2742G>A | p.Thr914= | synonymous_variant | 20/23 | ENST00000361216.8 | |
ATP1A2 | XM_047421286.1 | c.1851G>A | p.Thr617= | synonymous_variant | 13/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP1A2 | ENST00000361216.8 | c.2742G>A | p.Thr914= | synonymous_variant | 20/23 | 1 | NM_000702.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251412Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135864
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461892Hom.: 0 Cov.: 34 AF XY: 0.0000110 AC XY: 8AN XY: 727246
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74438
ClinVar
Submissions by phenotype
Familial hemiplegic migraine Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 23, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at