2-28541711-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153021.5(PLB1):c.779C>T(p.Ala260Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,544 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_153021.5 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 |
---|---|---|---|---|---|---|---|
PLB1 | NM_153021.5 | c.779C>T | p.Ala260Val | missense_variant | 13/58 | ENST00000327757.10 | |
PLB1 | NM_001170585.2 | c.812C>T | p.Ala271Val | missense_variant | 13/57 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLB1 | ENST00000327757.10 | c.779C>T | p.Ala260Val | missense_variant | 13/58 | 1 | NM_153021.5 | P1 | |
PLB1 | ENST00000422425.6 | c.812C>T | p.Ala271Val | missense_variant | 13/57 | 1 | |||
PLB1 | ENST00000404858.5 | c.809C>T | p.Ala270Val | missense_variant | 13/57 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250452Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135384
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461372Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726988
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 09, 2021 | The c.779C>T (p.A260V) alteration is located in exon 13 (coding exon 13) of the PLB1 gene. This alteration results from a C to T substitution at nucleotide position 779, causing the alanine (A) at amino acid position 260 to be replaced by a valine (V). 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