rs977911026
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017871.6(INTS11):āc.1616A>Gā(p.Lys539Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000059 in 1,525,296 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_017871.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000156 AC: 2AN: 128312Hom.: 0 Cov.: 23
GnomAD3 exomes AF: 0.0000203 AC: 4AN: 197504Hom.: 0 AF XY: 0.00000940 AC XY: 1AN XY: 106354
GnomAD4 exome AF: 0.00000501 AC: 7AN: 1396984Hom.: 0 Cov.: 35 AF XY: 0.00000436 AC XY: 3AN XY: 687858
GnomAD4 genome AF: 0.0000156 AC: 2AN: 128312Hom.: 0 Cov.: 23 AF XY: 0.0000335 AC XY: 2AN XY: 59764
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1616A>G (p.K539R) alteration is located in exon 16 (coding exon 16) of the CPSF3L gene. This alteration results from a A to G substitution at nucleotide position 1616, causing the lysine (K) at amino acid position 539 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