rs55858252
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_000702.4(ATP1A2):c.25T>A(p.Tyr9Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00303 in 1,596,846 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000702.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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ATP1A2 | NM_000702.4 | c.25T>A | p.Tyr9Asn | missense_variant | Exon 2 of 23 | ENST00000361216.8 | NP_000693.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP1A2 | ENST00000361216.8 | c.25T>A | p.Tyr9Asn | missense_variant | Exon 2 of 23 | 1 | NM_000702.4 | ENSP00000354490.3 | ||
ATP1A2 | ENST00000392233.7 | c.25T>A | p.Tyr9Asn | missense_variant | Exon 2 of 23 | 5 | ENSP00000376066.3 | |||
ATP1A2 | ENST00000472488.5 | n.128T>A | non_coding_transcript_exon_variant | Exon 2 of 20 | 2 | |||||
ATP1A2 | ENST00000478587.1 | n.124T>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00210 AC: 319AN: 152012Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00170 AC: 365AN: 214772Hom.: 0 AF XY: 0.00174 AC XY: 202AN XY: 116084
GnomAD4 exome AF: 0.00313 AC: 4523AN: 1444716Hom.: 9 Cov.: 34 AF XY: 0.00305 AC XY: 2191AN XY: 717300
GnomAD4 genome AF: 0.00210 AC: 319AN: 152130Hom.: 1 Cov.: 33 AF XY: 0.00196 AC XY: 146AN XY: 74354
ClinVar
Submissions by phenotype
not provided Benign:4
This variant is associated with the following publications: (PMID: 18957371, 27445835, 18513263, 23954377, 20981092, 17877748, 21533730, 27226003) -
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ATP1A2: BS3:Supporting, BS2 -
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Migraine, familial hemiplegic, 2 Benign:2
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
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Alternating hemiplegia of childhood 1 Benign:2
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
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not specified Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Fetal akinesia, respiratory insufficiency, microcephaly, polymicrogyria, and dysmorphic facies Benign:1
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Developmental and epileptic encephalopathy 98 Benign:1
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Familial hemiplegic migraine Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at