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GeneBe

1-42545555-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001395517.1(CCDC30):c.866G>A(p.Arg289Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000117 in 1,453,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.000012 ( 0 hom. )

Consequence

CCDC30
NM_001395517.1 missense

Scores

1
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.482
Variant links:
Genes affected
CCDC30 (HGNC:26103): (coiled-coil domain containing 30)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.04437852).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCDC30NM_001395517.1 linkuse as main transcriptc.866G>A p.Arg289Gln missense_variant 9/21 ENST00000657597.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCDC30ENST00000657597.2 linkuse as main transcriptc.866G>A p.Arg289Gln missense_variant 9/21 NM_001395517.1 A2

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
0.0000117
AC:
17
AN:
1453852
Hom.:
0
Cov.:
30
AF XY:
0.0000138
AC XY:
10
AN XY:
723104
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000237
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000135
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31
Bravo
AF:
0.00000378
ExAC
AF:
0.00000824
AC:
1

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 submitterclinical testingAmbry GeneticsMay 06, 2022The c.401G>A (p.R134Q) alteration is located in exon 4 (coding exon 3) of the CCDC30 gene. This alteration results from a G to A substitution at nucleotide position 401, causing the arginine (R) at amino acid position 134 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.076
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.68
Cadd
Benign
17
Dann
Uncertain
0.99
Eigen
Benign
-0.78
Eigen_PC
Benign
-0.60
FATHMM_MKL
Benign
0.34
N
LIST_S2
Benign
0.62
T;T;.
M_CAP
Benign
0.0098
T
MetaRNN
Benign
0.044
T;T;T
MetaSVM
Benign
-1.1
T
MutationTaster
Benign
1.0
D;D;N;N;N
PrimateAI
Benign
0.33
T
REVEL
Benign
0.028
Polyphen
0.0070
.;B;B
Vest4
0.11
MutPred
0.11
.;Gain of helix (P = 0.132);Gain of helix (P = 0.132);
MVP
0.030
MPC
0.27
ClinPred
0.096
T
GERP RS
2.9
Varity_R
0.037
gMVP
0.066

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs771159252; hg19: chr1-43011226; COSMIC: COSV59605287; API