1-42539195-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001395517.1(CCDC30):c.605A>G(p.Glu202Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000533 in 1,594,136 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 (★).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000036 ( 0 hom. )
Consequence
CCDC30
NM_001395517.1 missense
NM_001395517.1 missense
Scores
1
8
5
Clinical Significance
Conservation
PhyloP100: 4.90
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.30017567).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC30 | NM_001395517.1 | c.605A>G | p.Glu202Gly | missense_variant | 8/21 | ENST00000657597.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC30 | ENST00000657597.2 | c.605A>G | p.Glu202Gly | missense_variant | 8/21 | NM_001395517.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152214Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
33
AN:
152214
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000630 AC: 15AN: 238022Hom.: 0 AF XY: 0.0000543 AC XY: 7AN XY: 128884
GnomAD3 exomes
AF:
AC:
15
AN:
238022
Hom.:
AF XY:
AC XY:
7
AN XY:
128884
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000361 AC: 52AN: 1441922Hom.: 0 Cov.: 29 AF XY: 0.0000307 AC XY: 22AN XY: 716706
GnomAD4 exome
AF:
AC:
52
AN:
1441922
Hom.:
Cov.:
29
AF XY:
AC XY:
22
AN XY:
716706
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20AN XY: 74368
GnomAD4 genome
?
AF:
AC:
33
AN:
152214
Hom.:
Cov.:
32
AF XY:
AC XY:
20
AN XY:
74368
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
2
ESP6500EA
AF:
AC:
0
ExAC
?
AF:
AC:
8
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | The c.140A>G (p.E47G) alteration is located in exon 3 (coding exon 2) of the CCDC30 gene. This alteration results from a A to G substitution at nucleotide position 140, causing the glutamic acid (E) at amino acid position 47 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Pathogenic
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;.
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
REVEL
Uncertain
Polyphen
1.0
.;D;D
Vest4
0.81, 0.83
MVP
MPC
0.82
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at