chr12-89603718-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP2PP3_Moderate
The NM_001366521.1(ATP2B1):c.2842T>A(p.Phe948Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,532 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001366521.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2B1 | NM_001366521.1 | c.2842T>A | p.Phe948Ile | missense_variant | 17/21 | ENST00000428670.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2B1 | ENST00000428670.8 | c.2842T>A | p.Phe948Ile | missense_variant | 17/21 | 5 | NM_001366521.1 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250700Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135466
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459532Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726242
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 23, 2023 | The c.2842T>A (p.F948I) alteration is located in exon 16 (coding exon 16) of the ATP2B1 gene. This alteration results from a T to A substitution at nucleotide position 2842, causing the phenylalanine (F) at amino acid position 948 to be replaced by an isoleucine (I). 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