chrX-49064547-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001163321.4(CCDC120):​c.607C>G​(p.Arg203Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000094 in 1,064,037 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R203W) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 23)
Exomes š‘“: 9.4e-7 ( 0 hom. 0 hem. )

Consequence

CCDC120
NM_001163321.4 missense

Scores

1
9
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.22
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC120NM_001163321.4 linkc.607C>G p.Arg203Gly 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.607C>G p.Arg203Gly missense_variant Exon 6 of 11 2 NM_001163321.4 ENSP00000474071.1 Q96HB5-4

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
AF:
9.40e-7
AC:
1
AN:
1064037
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
346301
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000121
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.37
BayesDel_addAF
Uncertain
0.15
D
BayesDel_noAF
Uncertain
-0.030
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.46
T;T;T;.;.
FATHMM_MKL
Benign
0.65
D
LIST_S2
Benign
0.81
.;.;T;T;T
M_CAP
Benign
0.052
D
MetaRNN
Uncertain
0.57
D;D;D;D;D
MetaSVM
Benign
-0.80
T
MutationAssessor
Uncertain
2.4
M;M;M;.;.
PrimateAI
Uncertain
0.70
T
PROVEAN
Pathogenic
-5.2
.;.;.;.;D
REVEL
Benign
0.17
Sift
Uncertain
0.0010
.;.;.;.;D
Sift4G
Benign
0.19
T;T;T;T;T
Polyphen
0.18
B;B;B;.;.
Vest4
0.59
MutPred
0.40
Loss of helix (P = 0.0104);Loss of helix (P = 0.0104);Loss of helix (P = 0.0104);.;.;
MVP
0.27
ClinPred
0.98
D
GERP RS
3.5
Varity_R
0.60
gMVP
0.89

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-48922078; API