rs8102086
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004886.4(APBA3):āc.1126T>Gā(p.Cys376Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00755 in 1,613,188 control chromosomes in the GnomAD database, including 740 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C376R) has been classified as Likely benign.
Frequency
Consequence
NM_004886.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APBA3 | NM_004886.4 | c.1126T>G | p.Cys376Gly | missense_variant | 7/11 | ENST00000316757.4 | |
APBA3 | XM_006722950.5 | c.1126T>G | p.Cys376Gly | missense_variant | 7/10 | ||
APBA3 | XM_006722951.4 | c.400T>G | p.Cys134Gly | missense_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APBA3 | ENST00000316757.4 | c.1126T>G | p.Cys376Gly | missense_variant | 7/11 | 1 | NM_004886.4 | P1 | |
APBA3 | ENST00000590064.1 | n.3397T>G | non_coding_transcript_exon_variant | 1/4 | 1 | ||||
APBA3 | ENST00000588984.5 | n.970T>G | non_coding_transcript_exon_variant | 4/8 | 2 | ||||
APBA3 | ENST00000592826.1 | n.400T>G | non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0378 AC: 5748AN: 152030Hom.: 390 Cov.: 34
GnomAD3 exomes AF: 0.0102 AC: 2556AN: 249796Hom.: 151 AF XY: 0.00756 AC XY: 1023AN XY: 135406
GnomAD4 exome AF: 0.00439 AC: 6414AN: 1461040Hom.: 346 Cov.: 72 AF XY: 0.00389 AC XY: 2825AN XY: 726858
GnomAD4 genome ? AF: 0.0379 AC: 5768AN: 152148Hom.: 394 Cov.: 34 AF XY: 0.0354 AC XY: 2636AN XY: 74370
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at