13-72792477-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006346.4(PIBF1):c.283G>A(p.Ala95Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000286 in 1,572,822 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_006346.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIBF1 | NM_006346.4 | c.283G>A | p.Ala95Thr | missense_variant | 3/18 | ENST00000326291.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIBF1 | ENST00000326291.11 | c.283G>A | p.Ala95Thr | missense_variant | 3/18 | 1 | NM_006346.4 | P1 | |
PIBF1 | ENST00000617689.4 | c.283G>A | p.Ala95Thr | missense_variant | 3/16 | 1 | |||
PIBF1 | ENST00000615625.1 | c.-262+10128G>A | intron_variant | 1 | |||||
PIBF1 | ENST00000489797.1 | n.227G>A | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152054Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000546 AC: 12AN: 219920Hom.: 0 AF XY: 0.0000587 AC XY: 7AN XY: 119262
GnomAD4 exome AF: 0.0000253 AC: 36AN: 1420768Hom.: 0 Cov.: 27 AF XY: 0.0000241 AC XY: 17AN XY: 706026
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152054Hom.: 0 Cov.: 31 AF XY: 0.0000808 AC XY: 6AN XY: 74274
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2021 | The c.283G>A (p.A95T) alteration is located in exon 3 (coding exon 2) of the PIBF1 gene. This alteration results from a G to A substitution at nucleotide position 283, causing the alanine (A) at amino acid position 95 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