chr11-60842707-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024098.4(CCDC86):c.583C>T(p.Pro195Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,613,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024098.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC86 | NM_024098.4 | c.583C>T | p.Pro195Ser | missense_variant | 1/4 | ENST00000227520.10 | NP_077003.1 | |
CCDC86-AS1 | NR_182293.1 | n.317-727G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC86 | ENST00000227520.10 | c.583C>T | p.Pro195Ser | missense_variant | 1/4 | 1 | NM_024098.4 | ENSP00000227520 | P1 | |
ENST00000539897.1 | n.259G>A | non_coding_transcript_exon_variant | 1/2 | 4 | ||||||
CCDC86-AS1 | ENST00000538705.1 | n.317-727G>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
CCDC86 | ENST00000535217.1 | c.*2C>T | 3_prime_UTR_variant, NMD_transcript_variant | 2/5 | 5 | ENSP00000442111 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000442 AC: 11AN: 248808Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135104
GnomAD4 exome AF: 0.000133 AC: 195AN: 1461400Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 98AN XY: 726970
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 09, 2023 | The c.583C>T (p.P195S) alteration is located in exon 1 (coding exon 1) of the CCDC86 gene. This alteration results from a C to T substitution at nucleotide position 583, causing the proline (P) at amino acid position 195 to be replaced by a serine (S). 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