1-1312116-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_017871.6(INTS11):c.1639C>A(p.Pro547Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000209 in 1,575,368 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P547R) has been classified as Uncertain significance.
Frequency
Consequence
NM_017871.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150074Hom.: 0 Cov.: 25
GnomAD4 exome AF: 0.0000217 AC: 31AN: 1425294Hom.: 0 Cov.: 35 AF XY: 0.0000213 AC XY: 15AN XY: 704600
GnomAD4 genome AF: 0.0000133 AC: 2AN: 150074Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 73084
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1639C>A (p.P547T) alteration is located in exon 16 (coding exon 16) of the CPSF3L gene. This alteration results from a C to A substitution at nucleotide position 1639, causing the proline (P) at amino acid position 547 to be replaced by a threonine (T). 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