rs1555462180
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007347.5(AP4E1):c.2227C>G(p.Gln743Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,720 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 Uncertain significance (★).
Frequency
Consequence
NM_007347.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP4E1 | NM_007347.5 | c.2227C>G | p.Gln743Glu | missense_variant | 17/21 | ENST00000261842.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP4E1 | ENST00000261842.10 | c.2227C>G | p.Gln743Glu | missense_variant | 17/21 | 1 | NM_007347.5 | P1 | |
AP4E1 | ENST00000560508.1 | c.2002C>G | p.Gln668Glu | missense_variant | 17/21 | 1 | |||
AP4E1 | ENST00000558439.5 | c.*1351C>G | 3_prime_UTR_variant, NMD_transcript_variant | 17/21 | 1 | ||||
AP4E1 | ENST00000561393.5 | c.*1271C>G | 3_prime_UTR_variant, NMD_transcript_variant | 16/20 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461720Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727160
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 06, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at