NM_017871.6:c.1540C>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_017871.6(INTS11):c.1540C>T(p.Arg514Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000031 in 1,550,404 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R514R) has been classified as Likely benign.
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 AF: 0.0000527 AC: 8AN: 151858Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000383 AC: 6AN: 156750Hom.: 0 AF XY: 0.0000241 AC XY: 2AN XY: 82834
GnomAD4 exome AF: 0.0000286 AC: 40AN: 1398546Hom.: 0 Cov.: 36 AF XY: 0.0000246 AC XY: 17AN XY: 689900
GnomAD4 genome AF: 0.0000527 AC: 8AN: 151858Hom.: 0 Cov.: 33 AF XY: 0.0000674 AC XY: 5AN XY: 74144
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1540C>T (p.R514C) alteration is located in exon 15 (coding exon 15) of the CPSF3L gene. This alteration results from a C to T substitution at nucleotide position 1540, causing the arginine (R) at amino acid position 514 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