8-37762708-T-C
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_007198.4(PLPBP):āc.49T>Cā(p.Leu17=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000289 in 1,590,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.000026 ( 0 hom., cov: 32)
Exomes š: 0.000029 ( 0 hom. )
Consequence
PLPBP
NM_007198.4 synonymous
NM_007198.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.158
Genes affected
PLPBP (HGNC:9457): (pyridoxal phosphate binding protein) This gene encodes a pyridoxal 5'-phosphate binding protein involved in the homeostatic regulation of intracellular pyridoxal 5'-phosphate. This gene has a tumor suppressive effect on hepatocellular carcinoma and other solid tumors of epithelial origin. Naturally occurring mutations in this gene are associated with a pyridoxine-dependent epilepsy. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 8-37762708-T-C is Benign according to our data. Variant chr8-37762708-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 744006.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.158 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLPBP | NM_007198.4 | c.49T>C | p.Leu17= | synonymous_variant | 1/8 | ENST00000328195.8 | |
LOC124901934 | XR_007060889.1 | n.444A>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLPBP | ENST00000328195.8 | c.49T>C | p.Leu17= | synonymous_variant | 1/8 | 1 | NM_007198.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152028Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000336 AC: 7AN: 208260Hom.: 0 AF XY: 0.0000442 AC XY: 5AN XY: 113168
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GnomAD4 exome AF: 0.0000292 AC: 42AN: 1438640Hom.: 0 Cov.: 34 AF XY: 0.0000336 AC XY: 24AN XY: 714262
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152028Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74258
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at