chr15-50958637-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_007347.5(AP4E1):c.1694C>A(p.Ala565Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,614,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A565V) has been classified as Likely benign.
Frequency
Consequence
NM_007347.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP4E1 | NM_007347.5 | c.1694C>A | p.Ala565Glu | missense_variant | 14/21 | ENST00000261842.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP4E1 | ENST00000261842.10 | c.1694C>A | p.Ala565Glu | missense_variant | 14/21 | 1 | NM_007347.5 | P1 | |
AP4E1 | ENST00000560508.1 | c.1469C>A | p.Ala490Glu | missense_variant | 14/21 | 1 | |||
AP4E1 | ENST00000558439.5 | c.*818C>A | 3_prime_UTR_variant, NMD_transcript_variant | 14/21 | 1 | ||||
AP4E1 | ENST00000561393.5 | c.*738C>A | 3_prime_UTR_variant, NMD_transcript_variant | 13/20 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000736 AC: 112AN: 152176Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000171 AC: 43AN: 251322Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135824
GnomAD4 exome AF: 0.0000602 AC: 88AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.0000536 AC XY: 39AN XY: 727220
GnomAD4 genome AF: 0.000742 AC: 113AN: 152294Hom.: 0 Cov.: 31 AF XY: 0.000671 AC XY: 50AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 01, 2016 | - - |
Spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at