chr17-73254002-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001129885.1(CPSF4L):āc.332C>Gā(p.Ser111Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000451 in 1,551,422 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001129885.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPSF4L | NM_001129885.1 | c.332C>G | p.Ser111Cys | missense_variant | 4/6 | ENST00000344935.8 | |
CPSF4L | XM_011525115.3 | c.398C>G | p.Ser133Cys | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPSF4L | ENST00000344935.8 | c.332C>G | p.Ser111Cys | missense_variant | 4/6 | 1 | NM_001129885.1 | P1 | |
CPSF4L | ENST00000397671.1 | c.140C>G | p.Ser47Cys | missense_variant | 4/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152222Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000286 AC: 4AN: 1399200Hom.: 0 Cov.: 30 AF XY: 0.00000435 AC XY: 3AN XY: 690130
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 2022 | The c.332C>G (p.S111C) alteration is located in exon 4 (coding exon 4) of the CPSF4L gene. This alteration results from a C to G substitution at nucleotide position 332, causing the serine (S) at amino acid position 111 to be replaced by a cysteine (C). 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