rs1247159417
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001317163.2(C5):c.63C>T(p.Phe21Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
C5
NM_001317163.2 synonymous
NM_001317163.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.78
Publications
0 publications found
Genes affected
C5 (HGNC:1331): (complement C5) This gene encodes a component of the complement system, a part of the innate immune system that plays an important role in inflammation, host homeostasis, and host defense against pathogens. The encoded preproprotein is proteolytically processed to generate multiple protein products, including the C5 alpha chain, C5 beta chain, C5a anaphylatoxin and C5b. The C5 protein is comprised of the C5 alpha and beta chains, which are linked by a disulfide bridge. Cleavage of the alpha chain by a convertase enzyme results in the formation of the C5a anaphylatoxin, which possesses potent spasmogenic and chemotactic activity, and the C5b macromolecular cleavage product, a subunit of the membrane attack complex (MAC). Mutations in this gene cause complement component 5 deficiency, a disease characterized by recurrent bacterial infections. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2015]
CNTRL (HGNC:1858): (centriolin) This gene encodes a centrosomal protein required for the centrosome to function as a microtubule organizing center. The gene product is also associated with centrosome maturation. One version of stem cell myeloproliferative disorder is the result of a reciprocal translocation between chromosomes 8 and 9, with the breakpoint associated with fibroblast growth factor receptor 1 and centrosomal protein 1. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP7
Synonymous conserved (PhyloP=-1.78 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001317163.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| C5 | NM_001317163.2 | c.63C>T | p.Phe21Phe | synonymous | Exon 1 of 41 | NP_001304092.1 | A0A8Q3SID6 | ||
| CNTRL | NM_007018.6 | MANE Select | c.-498G>A | upstream_gene | N/A | NP_008949.4 | |||
| CNTRL | NM_001369893.1 | c.-325G>A | upstream_gene | N/A | NP_001356822.1 | Q5JVD1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| C5 | ENST00000696281.1 | c.63C>T | p.Phe21Phe | synonymous | Exon 1 of 42 | ENSP00000512521.1 | A0A8Q3SID6 | ||
| CNTRL | ENST00000690496.1 | n.-498G>A | non_coding_transcript_exon | Exon 1 of 18 | ENSP00000508719.1 | A0A8I5QL39 | |||
| C5 | ENST00000696279.1 | n.24C>T | non_coding_transcript_exon | Exon 1 of 43 | ENSP00000512520.1 | A0A8Q3SIH6 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152220
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 Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 301906Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 171952
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
301906
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
171952
African (AFR)
AF:
AC:
0
AN:
8558
American (AMR)
AF:
AC:
0
AN:
27226
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
10748
East Asian (EAS)
AF:
AC:
0
AN:
9204
South Asian (SAS)
AF:
AC:
0
AN:
59586
European-Finnish (FIN)
AF:
AC:
0
AN:
12298
Middle Eastern (MID)
AF:
AC:
0
AN:
1542
European-Non Finnish (NFE)
AF:
AC:
0
AN:
158664
Other (OTH)
AF:
AC:
0
AN:
14080
GnomAD4 genome 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74374 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152220
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
74374
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41446
American (AMR)
AF:
AC:
0
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5194
South Asian (SAS)
AF:
AC:
0
AN:
4832
European-Finnish (FIN)
AF:
AC:
0
AN:
10628
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68036
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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