2-56193189-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080433.2(CCDC85A):c.989G>C(p.Arg330Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000267 in 1,612,592 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
Genomes: 𝑓 0.00017 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
CCDC85A
NM_001080433.2 missense
NM_001080433.2 missense
Scores
4
15
Clinical Significance
Conservation
PhyloP100: 4.96
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.22285265).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC85A | NM_001080433.2 | c.989G>C | p.Arg330Thr | missense_variant | 2/6 | ENST00000407595.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC85A | ENST00000407595.3 | c.989G>C | p.Arg330Thr | missense_variant | 2/6 | 1 | NM_001080433.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000165 AC: 25AN: 151364Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000321 AC: 8AN: 248930Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135106
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GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461228Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726890
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GnomAD4 genome ? AF: 0.000165 AC: 25AN: 151364Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12AN XY: 73920
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2023 | The c.989G>C (p.R330T) alteration is located in exon 2 (coding exon 2) of the CCDC85A gene. This alteration results from a G to C substitution at nucleotide position 989, causing the arginine (R) at amino acid position 330 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at