chr15-29054387-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001353788.2(APBA2):c.503C>T(p.Pro168Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0008 in 1,614,122 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001353788.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APBA2 | NM_001353788.2 | c.503C>T | p.Pro168Leu | missense_variant | 4/15 | ENST00000683413.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APBA2 | ENST00000683413.1 | c.503C>T | p.Pro168Leu | missense_variant | 4/15 | NM_001353788.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00101 AC: 153AN: 152176Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00211 AC: 528AN: 250666Hom.: 9 AF XY: 0.00204 AC XY: 277AN XY: 135698
GnomAD4 exome AF: 0.000779 AC: 1139AN: 1461828Hom.: 18 Cov.: 33 AF XY: 0.000763 AC XY: 555AN XY: 727210
GnomAD4 genome ? AF: 0.00100 AC: 153AN: 152294Hom.: 2 Cov.: 33 AF XY: 0.000913 AC XY: 68AN XY: 74452
ClinVar
Submissions by phenotype
APBA2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 24, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at