rs1962149
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_172351.3(CD46):c.944-78G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 790,500 control chromosomes in the GnomAD database, including 54,689 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.36 ( 10056 hom., cov: 31)
Exomes 𝑓: 0.36 ( 44633 hom. )
Consequence
CD46
NM_172351.3 intron
NM_172351.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.311
Genes affected
CD46 (HGNC:6953): (CD46 molecule) The protein encoded by this gene is a type I membrane protein and is a regulatory part of the complement system. The encoded protein has cofactor activity for inactivation of complement components C3b and C4b by serum factor I, which protects the host cell from damage by complement. In addition, the encoded protein can act as a receptor for the Edmonston strain of measles virus, human herpesvirus-6, and type IV pili of pathogenic Neisseria. Finally, the protein encoded by this gene may be involved in the fusion of the spermatozoa with the oocyte during fertilization. Mutations at this locus have been associated with susceptibility to hemolytic uremic syndrome. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 1-207783214-G-A is Benign according to our data. Variant chr1-207783214-G-A is described in ClinVar as [Benign]. Clinvar id is 1242506.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-207783214-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD46 | NM_172351.3 | c.944-78G>A | intron_variant | ENST00000367042.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD46 | ENST00000367042.6 | c.944-78G>A | intron_variant | 1 | NM_172351.3 | A2 | |||
MIR29B2CHG | ENST00000710901.1 | n.663-20226C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.356 AC: 54011AN: 151700Hom.: 10046 Cov.: 31
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GnomAD4 exome AF: 0.362 AC: 231232AN: 638682Hom.: 44633 AF XY: 0.357 AC XY: 122596AN XY: 343442
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GnomAD4 genome ? AF: 0.356 AC: 54030AN: 151818Hom.: 10056 Cov.: 31 AF XY: 0.356 AC XY: 26413AN XY: 74206
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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 | GeneDx | Nov 11, 2018 | This variant is associated with the following publications: (PMID: 28939980) - |
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