1-1312115-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_017871.6(INTS11):āc.1640C>Gā(p.Pro547Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000014 in 1,424,658 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P547T) has been classified as Uncertain significance.
Frequency
Consequence
NM_017871.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 exomes AF: 0.0000197 AC: 4AN: 203216Hom.: 0 AF XY: 0.0000367 AC XY: 4AN XY: 109024
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1424658Hom.: 0 Cov.: 35 AF XY: 0.00000284 AC XY: 2AN XY: 704208
GnomAD4 genome Cov.: 25
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1640C>G (p.P547R) alteration is located in exon 16 (coding exon 16) of the CPSF3L gene. This alteration results from a C to G substitution at nucleotide position 1640, causing the proline (P) at amino acid position 547 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