chr5-14143778-C-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_007118.4(TRIO):c.53C>G(p.Ala18Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000983 in 1,017,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007118.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIO | NM_007118.4 | c.53C>G | p.Ala18Gly | missense_variant | 1/57 | ENST00000344204.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIO | ENST00000344204.9 | c.53C>G | p.Ala18Gly | missense_variant | 1/57 | 1 | NM_007118.4 | P1 | |
TRIO | ENST00000698541.1 | c.53C>G | p.Ala18Gly | missense_variant | 1/37 | ||||
TRIO | ENST00000502816.1 | n.77C>G | non_coding_transcript_exon_variant | 1/5 | 2 | ||||
TRIO | ENST00000505971.5 | n.77C>G | non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000136 AC: 2AN: 146578Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000919 AC: 8AN: 870526Hom.: 0 Cov.: 29 AF XY: 0.0000173 AC XY: 7AN XY: 405256
GnomAD4 genome ? AF: 0.0000136 AC: 2AN: 146578Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 71310
ClinVar
Submissions by phenotype
Micrognathia-recurrent infections-behavioral abnormalities-mild intellectual disability syndrome;C5394205:Intellectual developmental disorder, autosomal dominant 63, with macrocephaly Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Feb 26, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at