chr3-46976723-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_001277074.2(CCDC12):​c.10A>G​(p.Thr4Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 35)

Consequence

CCDC12
NM_001277074.2 missense

Scores

19

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.42
Variant links:
Genes affected
CCDC12 (HGNC:28332): (coiled-coil domain containing 12) Predicted to be part of U2-type spliceosomal complex and post-mRNA release spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.04070452).
BP6
Variant 3-46976723-T-C is Benign according to our data. Variant chr3-46976723-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3138287.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCDC12NM_001277074.2 linkuse as main transcriptc.10A>G p.Thr4Ala missense_variant 1/7 ENST00000683445.1 NP_001264003.1
CCDC12NM_144716.6 linkuse as main transcriptc.49A>G p.Thr17Ala missense_variant 2/8 NP_653317.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCDC12ENST00000683445.1 linkuse as main transcriptc.10A>G p.Thr4Ala missense_variant 1/7 NM_001277074.2 ENSP00000508011 P1

Frequencies

GnomAD3 genomes
Cov.:
35
GnomAD4 exome
Cov.:
57
GnomAD4 genome
Cov.:
35

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsFeb 05, 2024This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.053
BayesDel_addAF
Benign
-0.36
T
BayesDel_noAF
Benign
-0.75
CADD
Benign
0.0070
DANN
Benign
0.75
DEOGEN2
Benign
0.0065
T;.;T;T
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.0030
N
LIST_S2
Benign
0.33
T;T;T;T
M_CAP
Benign
0.0018
T
MetaRNN
Benign
0.041
T;T;T;T
MetaSVM
Benign
-0.98
T
MutationAssessor
Benign
-0.69
N;.;.;.
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Benign
0.35
T
PROVEAN
Benign
-0.47
.;N;.;.
REVEL
Benign
0.012
Sift
Benign
0.23
.;T;.;.
Sift4G
Benign
0.57
T;T;T;.
Polyphen
0.0
B;.;.;.
Vest4
0.034
MutPred
0.18
Gain of helix (P = 0.0093);.;Gain of helix (P = 0.0093);Gain of helix (P = 0.0093);
MVP
0.10
MPC
0.21
ClinPred
0.086
T
GERP RS
-4.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.026
gMVP
0.11

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-47018213; API