15-50908808-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_007347.5(AP4E1):c.30G>T(p.Thr10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,448,258 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T10T) 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 -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP4E1 | NM_007347.5 | c.30G>T | p.Thr10= | synonymous_variant | 1/21 | ENST00000261842.10 | |
AP4E1 | NM_001252127.2 | c.-219G>T | 5_prime_UTR_variant | 1/21 | |||
AP4E1 | XM_005254264.5 | c.-76+165G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP4E1 | ENST00000261842.10 | c.30G>T | p.Thr10= | synonymous_variant | 1/21 | 1 | NM_007347.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000461 AC: 1AN: 216922Hom.: 0 AF XY: 0.00000840 AC XY: 1AN XY: 119076
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1448258Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 719342
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at