1-162859577-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001394065.1(CCDC190):c.70G>A(p.Ala24Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000458 in 1,461,610 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000046 ( 1 hom. )
Consequence
CCDC190
NM_001394065.1 missense
NM_001394065.1 missense
Scores
2
2
12
Clinical Significance
Conservation
PhyloP100: 1.45
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=0.117949545).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC190 | NM_001394065.1 | c.70G>A | p.Ala24Thr | missense_variant | 2/4 | ENST00000367912.7 | |
CCDC190 | NM_178550.6 | c.70G>A | p.Ala24Thr | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC190 | ENST00000367912.7 | c.70G>A | p.Ala24Thr | missense_variant | 2/4 | 5 | NM_001394065.1 | A2 | |
CCDC190 | ENST00000367910.5 | c.70G>A | p.Ala24Thr | missense_variant | 2/4 | 2 | P4 | ||
CCDC190 | ENST00000367911.3 | c.70G>A | p.Ala24Thr | missense_variant | 1/3 | 3 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.0000522 AC: 13AN: 248900Hom.: 0 AF XY: 0.0000963 AC XY: 13AN XY: 135014
GnomAD3 exomes
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13
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248900
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135014
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GnomAD4 exome AF: 0.0000458 AC: 67AN: 1461610Hom.: 1 Cov.: 31 AF XY: 0.0000756 AC XY: 55AN XY: 727074
GnomAD4 exome
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1461610
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31
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727074
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ExAC
?
AF:
AC:
6
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 | Jul 06, 2021 | The c.70G>A (p.A24T) alteration is located in exon 2 (coding exon 1) of the CCDC190 gene. This alteration results from a G to A substitution at nucleotide position 70, causing the alanine (A) at amino acid position 24 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
Uncertain
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;.
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PROVEAN
Uncertain
D;.;D
REVEL
Benign
Sift
Pathogenic
D;.;D
Sift4G
Pathogenic
D;D;D
Polyphen
P;P;P
Vest4
MutPred
Gain of phosphorylation at A24 (P = 0.0441);Gain of phosphorylation at A24 (P = 0.0441);Gain of phosphorylation at A24 (P = 0.0441);
MVP
MPC
0.12
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
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Score
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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