12-69262539-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_007007.3(CPSF6):c.1636C>T(p.Arg546Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,176 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007007.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249908Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135156
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461176Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726908
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1636C>T (p.R546C) alteration is located in exon 9 (coding exon 9) of the CPSF6 gene. This alteration results from a C to T substitution at nucleotide position 1636, causing the arginine (R) at amino acid position 546 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