3-112638067-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_199511.3(CCDC80):c.1839C>G(p.Ala613=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000578 in 1,609,418 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00032 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000031 ( 1 hom. )
Consequence
CCDC80
NM_199511.3 synonymous
NM_199511.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.37
Genes affected
CCDC80 (HGNC:30649): (coiled-coil domain containing 80) Predicted to enable glycosaminoglycan binding activity. Predicted to act upstream of or within extracellular matrix organization; positive regulation of cell-substrate adhesion; and response to bacterium. Predicted to be located in extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 3-112638067-G-C is Benign according to our data. Variant chr3-112638067-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3234333.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.37 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC80 | NM_199511.3 | c.1839C>G | p.Ala613= | synonymous_variant | 2/8 | ENST00000206423.8 | |
CCDC80 | NM_199512.3 | c.1839C>G | p.Ala613= | synonymous_variant | 2/8 | ||
CCDC80 | XM_047447495.1 | c.1872C>G | p.Ala624= | synonymous_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC80 | ENST00000206423.8 | c.1839C>G | p.Ala613= | synonymous_variant | 2/8 | 1 | NM_199511.3 | P1 | |
CCDC80 | ENST00000439685.6 | c.1839C>G | p.Ala613= | synonymous_variant | 2/8 | 1 | P1 | ||
CCDC80 | ENST00000461431.1 | c.33C>G | p.Ala11= | synonymous_variant | 1/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000315 AC: 48AN: 152154Hom.: 0 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
48
AN:
152154
Hom.:
Cov.:
31
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: 0.000156 AC: 38AN: 244232Hom.: 0 AF XY: 0.000114 AC XY: 15AN XY: 132086
GnomAD3 exomes
AF:
AC:
38
AN:
244232
Hom.:
AF XY:
AC XY:
15
AN XY:
132086
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: 0.0000309 AC: 45AN: 1457264Hom.: 1 Cov.: 33 AF XY: 0.0000304 AC XY: 22AN XY: 724784
GnomAD4 exome
AF:
AC:
45
AN:
1457264
Hom.:
Cov.:
33
AF XY:
AC XY:
22
AN XY:
724784
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: 0.000315 AC: 48AN: 152154Hom.: 0 Cov.: 31 AF XY: 0.000296 AC XY: 22AN XY: 74340
GnomAD4 genome
?
AF:
AC:
48
AN:
152154
Hom.:
Cov.:
31
AF XY:
AC XY:
22
AN XY:
74340
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 | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | CCDC80: BP4, BP7 - |
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