rs1782455
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The ENST00000400897.8(MASP2):c.1479C>T(p.Ser493=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 1,613,586 control chromosomes in the GnomAD database, including 534,265 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.69 ( 39519 hom., cov: 31)
Exomes 𝑓: 0.82 ( 494746 hom. )
Consequence
MASP2
ENST00000400897.8 synonymous
ENST00000400897.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.31
Genes affected
MASP2 (HGNC:6902): (MBL associated serine protease 2) This gene encodes a member of the peptidase S1 family of serine proteases. The encoded preproprotein is proteolytically processed to generate A and B chains that heterodimerize to form the mature protease. This protease cleaves complement components C2 and C4 in order to generate C3 convertase in the lectin pathway of the complement system. The encoded protease also plays a role in the coagulation cascade through cleavage of prothrombin to form thrombin. Myocardial infarction and acute stroke patients exhibit reduced serum concentrations of the encoded protein. Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Feb 2016]
TARDBP (HGNC:11571): (TAR DNA binding protein) HIV-1, the causative agent of acquired immunodeficiency syndrome (AIDS), contains an RNA genome that produces a chromosomally integrated DNA during the replicative cycle. Activation of HIV-1 gene expression by the transactivator Tat is dependent on an RNA regulatory element (TAR) located downstream of the transcription initiation site. The protein encoded by this gene is a transcriptional repressor that binds to chromosomally integrated TAR DNA and represses HIV-1 transcription. In addition, this protein regulates alternate splicing of the CFTR gene. A similar pseudogene is present on chromosome 20. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 1-11027467-G-A is Benign according to our data. Variant chr1-11027467-G-A is described in ClinVar as [Benign]. Clinvar id is 291781.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-11027467-G-A is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-1.31 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MASP2 | NM_006610.4 | c.1479C>T | p.Ser493= | synonymous_variant | 11/11 | ENST00000400897.8 | NP_006601.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MASP2 | ENST00000400897.8 | c.1479C>T | p.Ser493= | synonymous_variant | 11/11 | 1 | NM_006610.4 | ENSP00000383690 | P1 |
Frequencies
GnomAD3 genomes AF: 0.689 AC: 104692AN: 151866Hom.: 39509 Cov.: 31
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GnomAD3 exomes AF: 0.793 AC: 199509AN: 251474Hom.: 81163 AF XY: 0.800 AC XY: 108673AN XY: 135910
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GnomAD4 exome AF: 0.818 AC: 1196308AN: 1461602Hom.: 494746 Cov.: 52 AF XY: 0.818 AC XY: 595118AN XY: 727126
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GnomAD4 genome AF: 0.689 AC: 104739AN: 151984Hom.: 39519 Cov.: 31 AF XY: 0.692 AC XY: 51388AN XY: 74284
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Immunodeficiency due to MASP-2 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Amyotrophic Lateral Sclerosis, Dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Frontotemporal dementia Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
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