15-55340668-A-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_004855.5(PIGB):c.903A>C(p.Thr301=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000589 in 1,613,010 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 (★). Synonymous variant affecting the same amino acid position (i.e. T301T) has been classified as Likely benign.
Frequency
Consequence
NM_004855.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGB | NM_004855.5 | c.903A>C | p.Thr301= | synonymous_variant | 8/12 | ENST00000164305.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGB | ENST00000164305.10 | c.903A>C | p.Thr301= | synonymous_variant | 8/12 | 1 | NM_004855.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000113 AC: 28AN: 247806Hom.: 0 AF XY: 0.000119 AC XY: 16AN XY: 134398
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1460858Hom.: 0 Cov.: 31 AF XY: 0.0000509 AC XY: 37AN XY: 726598
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74374
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at