chr19-2102184-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001261826.3(AP3D1):c.3637G>A(p.Ala1213Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,613,684 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_001261826.3 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 |
---|---|---|---|---|---|---|---|
AP3D1 | NM_001261826.3 | c.3637G>A | p.Ala1213Thr | missense_variant | 32/32 | ENST00000643116.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP3D1 | ENST00000643116.3 | c.3637G>A | p.Ala1213Thr | missense_variant | 32/32 | NM_001261826.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000302 AC: 46AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000803 AC: 20AN: 249116Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135220
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461358Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 727038
GnomAD4 genome ? AF: 0.000302 AC: 46AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74498
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1213 of the AP3D1 protein (p.Ala1213Thr). This variant is present in population databases (rs201113371, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with AP3D1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1440018). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Hermansky-Pudlak syndrome 10 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 26, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at