chr1-207114485-CT-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_000715.4(C4BPA):c.328+226del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.067 ( 13 hom., cov: 19)
Failed GnomAD Quality Control
Consequence
C4BPA
NM_000715.4 intron
NM_000715.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0460
Genes affected
C4BPA (HGNC:1325): (complement component 4 binding protein alpha) This gene encodes a member of a superfamily of proteins composed predominantly of tandemly arrayed short consensus repeats of approximately 60 amino acids. Along with a single, unique beta-chain, seven identical alpha-chains encoded by this gene assemble into the predominant isoform of C4b-binding protein, a multimeric protein that controls activation of the complement cascade through the classical pathway. The genes encoding both alpha and beta chains are located adjacent to each other on human chromosome 1 in the regulator of complement activation gene cluster. Two pseudogenes of this gene are also found in the cluster. [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.
BP6
?
Variant 1-207114485-CT-C is Benign according to our data. Variant chr1-207114485-CT-C is described in ClinVar as [Benign]. Clinvar id is 1249174.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C4BPA | NM_000715.4 | c.328+226del | intron_variant | ENST00000367070.8 | |||
C4BPA | XM_005273251.3 | c.328+226del | intron_variant | ||||
C4BPA | XM_005273252.5 | c.328+226del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C4BPA | ENST00000367070.8 | c.328+226del | intron_variant | 1 | NM_000715.4 | P1 | |||
C4BPA | ENST00000421786.5 | c.328+226del | intron_variant | 4 | |||||
C4BPA | ENST00000424088.1 | c.329-165del | intron_variant, NMD_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 3958AN: 59420Hom.: 13 Cov.: 19 FAILED QC
GnomAD3 genomes
?
AF:
AC:
3958
AN:
59420
Hom.:
Cov.:
19
FAILED QC
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0667 AC: 3961AN: 59408Hom.: 13 Cov.: 19 AF XY: 0.0624 AC XY: 1741AN XY: 27896
GnomAD4 genome
?
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
3961
AN:
59408
Hom.:
Cov.:
19
AF XY:
AC XY:
1741
AN XY:
27896
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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