chr15-55355419-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004855.5(PIGB):āc.1652A>Cā(p.Lys551Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00363 in 1,607,172 control chromosomes in the GnomAD database, including 178 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_004855.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIGB | ENST00000164305.10 | c.1652A>C | p.Lys551Thr | missense_variant | Exon 12 of 12 | 1 | NM_004855.5 | ENSP00000164305.5 | ||
CCPG1 | ENST00000442196 | c.*801T>G | 3_prime_UTR_variant | Exon 9 of 9 | 2 | NM_001204450.2 | ENSP00000403400.3 |
Frequencies
GnomAD3 genomes AF: 0.0197 AC: 2997AN: 152214Hom.: 88 Cov.: 32
GnomAD3 exomes AF: 0.00492 AC: 1180AN: 239680Hom.: 37 AF XY: 0.00368 AC XY: 479AN XY: 130104
GnomAD4 exome AF: 0.00193 AC: 2815AN: 1454840Hom.: 89 Cov.: 29 AF XY: 0.00160 AC XY: 1154AN XY: 723498
GnomAD4 genome AF: 0.0198 AC: 3013AN: 152332Hom.: 89 Cov.: 32 AF XY: 0.0193 AC XY: 1435AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 02, 2025 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
PIGB-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 12, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at