chr17-73261746-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001129885.1(CPSF4L):c.73A>C(p.Thr25Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. 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. T25N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001129885.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPSF4L | NM_001129885.1 | c.73A>C | p.Thr25Pro | missense_variant | 1/6 | ENST00000344935.8 | |
CPSF4L | XM_011525115.3 | c.139A>C | p.Thr47Pro | missense_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPSF4L | ENST00000344935.8 | c.73A>C | p.Thr25Pro | missense_variant | 1/6 | 1 | NM_001129885.1 | P1 | |
CPSF4L | ENST00000397671.1 | c.-90+363A>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | The c.73A>C (p.T25P) alteration is located in exon 1 (coding exon 1) of the CPSF4L gene. This alteration results from a A to C substitution at nucleotide position 73, causing the threonine (T) at amino acid position 25 to be replaced by a proline (P). 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