2-55291744-T-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_001365480.1(CCDC88A):c.5583A>T(p.Ser1861=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,612,700 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000092 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
CCDC88A
NM_001365480.1 synonymous
NM_001365480.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.10
Genes affected
CCDC88A (HGNC:25523): (coiled-coil domain containing 88A) This gene encodes a member of the Girdin family of coiled-coil domain containing proteins. The encoded protein is an actin-binding protein that is activated by the serine/threonine kinase Akt and plays a role in cytoskeleton remodeling and cell migration. The encoded protein also enhances Akt signaling by mediating phosphoinositide 3-kinase (PI3K)-dependent activation of Akt by growth factor receptor tyrosine kinases and G protein-coupled receptors. Increased expression of this gene and phosphorylation of the encoded protein may play a role in cancer metastasis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 2-55291744-T-A is Benign according to our data. Variant chr2-55291744-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 1648254.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=3.1 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000092 (14/152196) while in subpopulation AFR AF= 0.000338 (14/41460). AF 95% confidence interval is 0.000204. There are 0 homozygotes in gnomad4. There are 6 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88A | NM_001365480.1 | c.5583A>T | p.Ser1861= | synonymous_variant | 32/33 | ENST00000436346.7 | |
CCDC88A | NM_001135597.2 | c.5580A>T | p.Ser1860= | synonymous_variant | 32/33 | ||
CCDC88A | NM_018084.5 | c.5499A>T | p.Ser1833= | synonymous_variant | 31/32 | ||
CCDC88A | NM_001254943.2 | c.5358A>T | p.Ser1786= | synonymous_variant | 33/34 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88A | ENST00000436346.7 | c.5583A>T | p.Ser1861= | synonymous_variant | 32/33 | 5 | NM_001365480.1 | A1 | |
ENST00000625718.2 | n.85+9310T>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152196Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
14
AN:
152196
Hom.:
Cov.:
32
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:
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250410Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135406
GnomAD3 exomes
AF:
AC:
6
AN:
250410
Hom.:
AF XY:
AC XY:
4
AN XY:
135406
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460504Hom.: 0 Cov.: 28 AF XY: 0.00000688 AC XY: 5AN XY: 726588
GnomAD4 exome
AF:
AC:
10
AN:
1460504
Hom.:
Cov.:
28
AF XY:
AC XY:
5
AN XY:
726588
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: 0.0000920 AC: 14AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74350
GnomAD4 genome
?
AF:
AC:
14
AN:
152196
Hom.:
Cov.:
32
AF XY:
AC XY:
6
AN XY:
74350
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 28, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at