chr12-14511302-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024829.6(PLBD1):āc.1144A>Gā(p.Thr382Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000404 in 1,609,962 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 (ā ).
Frequency
Consequence
NM_024829.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLBD1 | NM_024829.6 | c.1144A>G | p.Thr382Ala | missense_variant | 8/11 | ENST00000240617.10 | NP_079105.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLBD1 | ENST00000240617.10 | c.1144A>G | p.Thr382Ala | missense_variant | 8/11 | 1 | NM_024829.6 | ENSP00000240617 | P1 | |
PLBD1 | ENST00000541800.6 | n.767A>G | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247820Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 133992
GnomAD4 exome AF: 0.0000295 AC: 43AN: 1457642Hom.: 0 Cov.: 33 AF XY: 0.0000248 AC XY: 18AN XY: 725156
GnomAD4 genome AF: 0.000144 AC: 22AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2024 | The c.1144A>G (p.T382A) alteration is located in exon 8 (coding exon 8) of the PLBD1 gene. This alteration results from a A to G substitution at nucleotide position 1144, causing the threonine (T) at amino acid position 382 to be replaced by an alanine (A). 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