chr19-47320392-C-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001736.4(C5AR1):c.615C>G(p.Val205=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00191 in 1,610,264 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0097 ( 28 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 36 hom. )
Consequence
C5AR1
NM_001736.4 synonymous
NM_001736.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.33
Genes affected
C5AR1 (HGNC:1338): (complement C5a receptor 1) Enables G protein-coupled receptor activity and complement component C5a receptor activity. Involved in several processes, including complement component C5a signaling pathway; mRNA transcription by RNA polymerase II; and positive regulation of ERK1 and ERK2 cascade. Located in apical part of cell and basolateral plasma membrane. Biomarker of Alzheimer's disease; asthma; chronic obstructive pulmonary disease; rhinitis; and severe acute respiratory syndrome. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.78).
BP6
?
Variant 19-47320392-C-G is Benign according to our data. Variant chr19-47320392-C-G is described in ClinVar as [Benign]. Clinvar id is 770291.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.33 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00972 (1481/152292) while in subpopulation AFR AF= 0.0335 (1391/41548). AF 95% confidence interval is 0.032. There are 28 homozygotes in gnomad4. There are 710 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 26 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C5AR1 | NM_001736.4 | c.615C>G | p.Val205= | synonymous_variant | 2/2 | ENST00000355085.4 | |
C5AR1 | XM_047439300.1 | c.717C>G | p.Val239= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C5AR1 | ENST00000355085.4 | c.615C>G | p.Val205= | synonymous_variant | 2/2 | 1 | NM_001736.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00962 AC: 1464AN: 152174Hom.: 26 Cov.: 32
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GnomAD3 exomes AF: 0.00269 AC: 668AN: 248642Hom.: 18 AF XY: 0.00200 AC XY: 269AN XY: 134698
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GnomAD4 exome AF: 0.00110 AC: 1600AN: 1457972Hom.: 36 Cov.: 78 AF XY: 0.000972 AC XY: 705AN XY: 725480
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GnomAD4 genome ? AF: 0.00972 AC: 1481AN: 152292Hom.: 28 Cov.: 32 AF XY: 0.00953 AC XY: 710AN XY: 74466
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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 | Jun 12, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at