rs34000044
Positions:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001737.5(C9):c.162C>T(p.Cys54=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000509 in 1,591,094 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 0.00024 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000031 ( 0 hom. )
Consequence
C9
NM_001737.5 synonymous
NM_001737.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.969
Genes affected
C9 (HGNC:1358): (complement C9) This gene encodes the final component of the complement system. It participates in the formation of the Membrane Attack Complex (MAC). The MAC assembles on bacterial membranes to form a pore, permitting disruption of bacterial membrane organization. Mutations in this gene cause component C9 deficiency. [provided by RefSeq, Feb 2009]
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=-0.55).
BP6
?
Variant 5-39342112-G-A is Benign according to our data. Variant chr5-39342112-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1174823.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-39342112-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=0.969 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C9 | NM_001737.5 | c.162C>T | p.Cys54= | synonymous_variant | 2/11 | ENST00000263408.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C9 | ENST00000263408.5 | c.162C>T | p.Cys54= | synonymous_variant | 2/11 | 1 | NM_001737.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000243 AC: 37AN: 152144Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
37
AN:
152144
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: 0.0000636 AC: 16AN: 251468Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135906
GnomAD3 exomes
AF:
AC:
16
AN:
251468
Hom.:
AF XY:
AC XY:
8
AN XY:
135906
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: 0.0000306 AC: 44AN: 1438832Hom.: 0 Cov.: 28 AF XY: 0.0000362 AC XY: 26AN XY: 717450
GnomAD4 exome
AF:
AC:
44
AN:
1438832
Hom.:
Cov.:
28
AF XY:
AC XY:
26
AN XY:
717450
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: 0.000243 AC: 37AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74460
GnomAD4 genome
?
AF:
AC:
37
AN:
152262
Hom.:
Cov.:
32
AF XY:
AC XY:
17
AN XY:
74460
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:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 10, 2023 | - - |
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
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