chr1-207113064-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_000715.4(C4BPA):āc.39A>Gā(p.Arg13=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00409 in 1,609,546 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0088 ( 8 hom., cov: 32)
Exomes š: 0.0036 ( 37 hom. )
Consequence
C4BPA
NM_000715.4 synonymous
NM_000715.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.175
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 1-207113064-A-G is Benign according to our data. Variant chr1-207113064-A-G is described in ClinVar as [Benign]. Clinvar id is 711057.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.175 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00879 (1338/152218) while in subpopulation AFR AF= 0.0232 (962/41538). AF 95% confidence interval is 0.0219. There are 8 homozygotes in gnomad4. There are 643 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C4BPA | NM_000715.4 | c.39A>G | p.Arg13= | synonymous_variant | 2/12 | ENST00000367070.8 | |
C4BPA | XM_005273251.3 | c.39A>G | p.Arg13= | synonymous_variant | 2/12 | ||
C4BPA | XM_005273252.5 | c.39A>G | p.Arg13= | synonymous_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C4BPA | ENST00000367070.8 | c.39A>G | p.Arg13= | synonymous_variant | 2/12 | 1 | NM_000715.4 | P1 | |
C4BPA | ENST00000421786.5 | c.39A>G | p.Arg13= | synonymous_variant | 2/5 | 4 | |||
C4BPA | ENST00000424088.1 | c.39A>G | p.Arg13= | synonymous_variant, NMD_transcript_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00878 AC: 1336AN: 152100Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00451 AC: 1107AN: 245598Hom.: 10 AF XY: 0.00424 AC XY: 564AN XY: 132924
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GnomAD4 exome AF: 0.00359 AC: 5238AN: 1457328Hom.: 37 Cov.: 31 AF XY: 0.00361 AC XY: 2615AN XY: 724956
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GnomAD4 genome AF: 0.00879 AC: 1338AN: 152218Hom.: 8 Cov.: 32 AF XY: 0.00864 AC XY: 643AN XY: 74426
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at