19-49130459-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_003660.4(PPFIA3):c.739G>A(p.Ala247Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000249 in 1,608,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003660.4 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 |
---|---|---|---|---|---|---|---|
PPFIA3 | NM_003660.4 | c.739G>A | p.Ala247Thr | missense_variant | 7/30 | ENST00000334186.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPFIA3 | ENST00000334186.9 | c.739G>A | p.Ala247Thr | missense_variant | 7/30 | 1 | NM_003660.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000428 AC: 1AN: 233552Hom.: 0 AF XY: 0.00000784 AC XY: 1AN XY: 127476
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1456376Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 723996
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74472
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2022 | The c.739G>A (p.A247T) alteration is located in exon 7 (coding exon 6) of the PPFIA3 gene. This alteration results from a G to A substitution at nucleotide position 739, causing the alanine (A) at amino acid position 247 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at