rs369028190
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_007347.5(AP4E1):c.1425G>A(p.Ala475=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000404 in 1,610,394 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A475A) has been classified as Likely benign.
Frequency
Consequence
NM_007347.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP4E1 | NM_007347.5 | c.1425G>A | p.Ala475= | synonymous_variant | 12/21 | ENST00000261842.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP4E1 | ENST00000261842.10 | c.1425G>A | p.Ala475= | synonymous_variant | 12/21 | 1 | NM_007347.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250928Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135588
GnomAD4 exome AF: 0.0000343 AC: 50AN: 1458250Hom.: 0 Cov.: 29 AF XY: 0.0000234 AC XY: 17AN XY: 725688
GnomAD4 genome ? AF: 0.0000986 AC: 15AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 11, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at