rs144750047
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001677.4(ATP1B1):c.-1C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000479 in 1,578,024 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001677.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00273 AC: 415AN: 152206Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000567 AC: 120AN: 211690Hom.: 0 AF XY: 0.000326 AC XY: 38AN XY: 116462
GnomAD4 exome AF: 0.000238 AC: 339AN: 1425710Hom.: 2 Cov.: 30 AF XY: 0.000209 AC XY: 148AN XY: 708938
GnomAD4 genome AF: 0.00274 AC: 417AN: 152314Hom.: 1 Cov.: 32 AF XY: 0.00267 AC XY: 199AN XY: 74468
ClinVar
Submissions by phenotype
not specified Benign:1
Variant summary: ATP1B1 c.-1C>A is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 0.00057 in 211690 control chromosomes, predominantly at a frequency of 0.0097 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 970 fold of the estimated maximal expected allele frequency for a pathogenic variant in ATP1B1 causing Arrhythmia phenotype (1e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. To our knowledge, no occurrence of c.-1C>A in individuals affected with Arrhythmia and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at