X-49064571-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001163321.4(CCDC120):​c.631C>T​(p.Leu211Phe) 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. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 23)

Consequence

CCDC120
NM_001163321.4 missense

Scores

3
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.285
Variant links:
Genes affected
CCDC120 (HGNC:28910): (coiled-coil domain containing 120) This gene encodes a protein that contains a coiled-coil domain. Several alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. [provided by RefSeq, Nov 2012]

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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=0.08602953).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC120NM_001163321.4 linkc.631C>T p.Leu211Phe missense_variant Exon 6 of 11 ENST00000603986.6 NP_001156793.2 Q96HB5-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC120ENST00000603986.6 linkc.631C>T p.Leu211Phe missense_variant Exon 6 of 11 2 NM_001163321.4 ENSP00000474071.1 Q96HB5-4

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
23

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Apr 04, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.526C>T (p.L176F) alteration is located in exon 6 (coding exon 4) of the CCDC120 gene. This alteration results from a C to T substitution at nucleotide position 526, causing the leucine (L) at amino acid position 176 to be replaced by a phenylalanine (F). 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
0.098
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.71
CADD
Benign
9.7
DANN
Uncertain
0.98
DEOGEN2
Benign
0.047
T;T;T;.;.
FATHMM_MKL
Benign
0.073
N
LIST_S2
Benign
0.72
.;.;T;T;T
M_CAP
Benign
0.0039
T
MetaRNN
Benign
0.086
T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.69
N;N;N;.;.
PrimateAI
Uncertain
0.51
T
PROVEAN
Benign
-0.64
.;.;.;.;N
REVEL
Benign
0.016
Sift
Uncertain
0.0080
.;.;.;.;D
Sift4G
Benign
0.079
T;T;T;T;T
Polyphen
0.23
B;B;B;.;.
Vest4
0.12
MutPred
0.27
Loss of disorder (P = 0.0599);Loss of disorder (P = 0.0599);Loss of disorder (P = 0.0599);.;.;
MVP
0.068
ClinPred
0.089
T
GERP RS
-1.3
Varity_R
0.17
gMVP
0.38

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: chrX-48922102; API