chr7-117721135-TAAAAA-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_033427.3(CTTNBP2):c.4448-10_4448-6delTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000193 in 1,550,998 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
CTTNBP2
NM_033427.3 splice_region, intron
NM_033427.3 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.09
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTTNBP2 | ENST00000160373.8 | c.4448-10_4448-6delTTTTT | splice_region_variant, intron_variant | Intron 19 of 22 | 1 | NM_033427.3 | ENSP00000160373.3 | |||
CTTNBP2 | ENST00000446636.5 | c.2909-10_2909-6delTTTTT | splice_region_variant, intron_variant | Intron 17 of 20 | 5 | ENSP00000389576.1 | ||||
CTTNBP2 | ENST00000441556.5 | n.*2362-10_*2362-6delTTTTT | splice_region_variant, intron_variant | Intron 19 of 22 | 5 | ENSP00000397678.1 | ||||
CTTNBP2 | ENST00000445366.1 | n.*165-10_*165-6delTTTTT | splice_region_variant, intron_variant | Intron 2 of 5 | 5 | ENSP00000389491.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33
GnomAD3 genomes
AF:
AC:
1
AN:
152208
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1398790Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 699720
GnomAD4 exome
AF:
AC:
2
AN:
1398790
Hom.:
AF XY:
AC XY:
0
AN XY:
699720
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74352
GnomAD4 genome
AF:
AC:
1
AN:
152208
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74352
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at