chr17-73252693-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001129885.1(CPSF4L):c.434G>A(p.Arg145Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,551,292 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 (★).
Frequency
Consequence
NM_001129885.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPSF4L | NM_001129885.1 | c.434G>A | p.Arg145Lys | missense_variant | 5/6 | ENST00000344935.8 | |
CPSF4L | XM_011525115.3 | c.500G>A | p.Arg167Lys | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPSF4L | ENST00000344935.8 | c.434G>A | p.Arg145Lys | missense_variant | 5/6 | 1 | NM_001129885.1 | P1 | |
CPSF4L | ENST00000397671.1 | c.245G>A | p.Arg82Lys | missense_variant | 5/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000167 AC: 26AN: 156110Hom.: 0 AF XY: 0.000218 AC XY: 18AN XY: 82732
GnomAD4 exome AF: 0.000101 AC: 141AN: 1399132Hom.: 0 Cov.: 30 AF XY: 0.000104 AC XY: 72AN XY: 690074
GnomAD4 genome AF: 0.000158 AC: 24AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.434G>A (p.R145K) alteration is located in exon 5 (coding exon 5) of the CPSF4L gene. This alteration results from a G to A substitution at nucleotide position 434, causing the arginine (R) at amino acid position 145 to be replaced by a lysine (K). 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