chr3-113978277-T-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020817.2(CCDC191):āc.2515A>Cā(p.Lys839Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000165 in 1,613,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000046 ( 0 hom., cov: 32)
Exomes š: 0.00018 ( 0 hom. )
Consequence
CCDC191
NM_020817.2 missense
NM_020817.2 missense
Scores
1
2
15
Clinical Significance
Conservation
PhyloP100: 4.66
Genes affected
CCDC191 (HGNC:29272): (coiled-coil domain containing 191)
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC191 | NM_020817.2 | c.2515A>C | p.Lys839Gln | missense_variant | 16/17 | ENST00000295878.8 | NP_065868.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC191 | ENST00000295878.8 | c.2515A>C | p.Lys839Gln | missense_variant | 16/17 | 1 | NM_020817.2 | ENSP00000295878 | P1 | |
CCDC191 | ENST00000460813.5 | downstream_gene_variant | 2 | ENSP00000418382 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152144Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250900Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135572
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GnomAD4 exome AF: 0.000178 AC: 260AN: 1461738Hom.: 0 Cov.: 31 AF XY: 0.000169 AC XY: 123AN XY: 727162
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74312
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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 | Oct 27, 2022 | The c.2515A>C (p.K839Q) alteration is located in exon 16 (coding exon 16) of the CCDC191 gene. This alteration results from a A to C substitution at nucleotide position 2515, causing the lysine (K) at amino acid position 839 to be replaced by a glutamine (Q). 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
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
B
Vest4
MutPred
Loss of methylation at K839 (P = 0.0442);
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
DS_AG_spliceai
Position offset: -3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at