chr12-49643272-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001031698.3(PRPF40B):āc.2255C>Gā(p.Pro752Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,614,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001031698.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRPF40B | NM_001031698.3 | c.2255C>G | p.Pro752Arg | missense_variant | 23/26 | ENST00000548825.7 | NP_001026868.2 | |
FMNL3 | NM_175736.5 | c.*2543G>C | 3_prime_UTR_variant | 26/26 | ENST00000335154.10 | NP_783863.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRPF40B | ENST00000548825.7 | c.2255C>G | p.Pro752Arg | missense_variant | 23/26 | 5 | NM_001031698.3 | ENSP00000448073 | P3 | |
FMNL3 | ENST00000335154.10 | c.*2543G>C | 3_prime_UTR_variant | 26/26 | 1 | NM_175736.5 | ENSP00000335655 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000642 AC: 16AN: 249038Hom.: 0 AF XY: 0.0000519 AC XY: 7AN XY: 134808
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461758Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727172
GnomAD4 genome AF: 0.000131 AC: 20AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 2023 | The c.2192C>G (p.P731R) alteration is located in exon 22 (coding exon 22) of the PRPF40B gene. This alteration results from a C to G substitution at nucleotide position 2192, causing the proline (P) at amino acid position 731 to be replaced by an arginine (R). 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