NM_178499.5:c.287A>C
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_178499.5(CCDC60):c.287A>C(p.Lys96Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,614,088 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178499.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.0000239 AC: 6AN: 251438 AF XY: 0.0000368 show subpopulations
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461882Hom.: 2 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727242 show subpopulations
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74368 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.287A>C (p.K96T) alteration is located in exon 3 (coding exon 3) of the CCDC60 gene. This alteration results from a A to C substitution at nucleotide position 287, causing the lysine (K) at amino acid position 96 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