chr4-42414656-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006095.2(ATP8A1):c.3368G>A(p.Arg1123His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,613,802 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_006095.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152084Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251256Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135790
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461600Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 727110
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74396
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3368G>A (p.R1123H) alteration is located in exon 36 (coding exon 36) of the ATP8A1 gene. This alteration results from a G to A substitution at nucleotide position 3368, causing the arginine (R) at amino acid position 1123 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at