chr21-45914500-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_001348241.2(PCBP3):c.667C>T(p.Arg223*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 216,964 control chromosomes in the GnomAD database, including 24,459 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001348241.2 stop_gained
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCBP3 | NM_001384156.1 | c.675+475C>T | intron_variant | Intron 12 of 17 | ENST00000681687.1 | NP_001371085.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.473 AC: 71916AN: 152050Hom.: 19105 Cov.: 34
GnomAD4 exome AF: 0.396 AC: 25627AN: 64796Hom.: 5323 Cov.: 0 AF XY: 0.394 AC XY: 12693AN XY: 32184
GnomAD4 genome AF: 0.473 AC: 71985AN: 152168Hom.: 19136 Cov.: 34 AF XY: 0.467 AC XY: 34713AN XY: 74396
ClinVar
Submissions by phenotype
PCBP3-related disorder Benign:1
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