chr11-118616199-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001144758.3(PHLDB1):c.343C>T(p.Arg115Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,613,742 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R115Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001144758.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHLDB1 | NM_001144758.3 | c.343C>T | p.Arg115Trp | missense_variant | 4/23 | ENST00000600882.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHLDB1 | ENST00000600882.6 | c.343C>T | p.Arg115Trp | missense_variant | 4/23 | 1 | NM_001144758.3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250058Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135302
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461562Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727098
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 27, 2023 | The c.343C>T (p.R115W) alteration is located in exon 5 (coding exon 3) of the PHLDB1 gene. This alteration results from a C to T substitution at nucleotide position 343, causing the arginine (R) at amino acid position 115 to be replaced by a tryptophan (W). 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