rs146299860

Variant summary

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

The NM_033427.3(CTTNBP2):​c.4687G>C​(p.Gly1563Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

CTTNBP2
NM_033427.3 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.722
Variant links:
Genes affected
CTTNBP2 (HGNC:15679): (cortactin binding protein 2) This gene encodes a protein with six ankyrin repeats and several proline-rich regions. A similar gene in rat interacts with a central regulator of the actin cytoskeleton. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

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=0.051383138).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CTTNBP2NM_033427.3 linkc.4687G>C p.Gly1563Arg missense_variant Exon 22 of 23 ENST00000160373.8 NP_219499.1 Q8WZ74Q20BG9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CTTNBP2ENST00000160373.8 linkc.4687G>C p.Gly1563Arg missense_variant Exon 22 of 23 1 NM_033427.3 ENSP00000160373.3 Q8WZ74

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461204
Hom.:
0
Cov.:
29
AF XY:
0.00000138
AC XY:
1
AN XY:
726910
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:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.074
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.40
CADD
Benign
16
DANN
Benign
0.71
DEOGEN2
Benign
0.012
T
Eigen
Benign
-0.26
Eigen_PC
Benign
-0.18
FATHMM_MKL
Benign
0.24
N
LIST_S2
Benign
0.78
T
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.051
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.18
N
PrimateAI
Benign
0.29
T
PROVEAN
Benign
-0.040
N
REVEL
Benign
0.13
Sift
Benign
0.79
T
Sift4G
Benign
0.76
T
Polyphen
0.0
B
Vest4
0.11
MutPred
0.13
Gain of solvent accessibility (P = 0.0037);
MVP
0.68
MPC
0.11
ClinPred
0.062
T
GERP RS
-0.29
Varity_R
0.051
gMVP
0.094

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: chr7-117358131; API