3-187220499-T-TC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001879.6(MASP1):c.1910-239_1910-238insG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00942 in 144,360 control chromosomes in the GnomAD database, including 26 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0094 ( 26 hom., cov: 30)
Consequence
MASP1
NM_001879.6 intron
NM_001879.6 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.129
Genes affected
MASP1 (HGNC:6901): (MBL associated serine protease 1) This gene encodes a serine protease that functions as a component of the lectin pathway of complement activation. The complement pathway plays an essential role in the innate and adaptive immune response. The encoded protein is synthesized as a zymogen and is activated when it complexes with the pathogen recognition molecules of lectin pathway, the mannose-binding lectin and the ficolins. This protein is not directly involved in complement activation but may play a role as an amplifier of complement activation by cleaving complement C2 or by activating another complement serine protease, MASP-2. The encoded protein is also able to cleave fibrinogen and factor XIII and may may be involved in coagulation. A splice variant of this gene which lacks the serine protease domain functions as an inhibitor of the complement pathway. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 3-187220499-T-TC is Benign according to our data. Variant chr3-187220499-T-TC is described in ClinVar as [Likely_benign]. Clinvar id is 1219212.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00942 (1360/144360) while in subpopulation AFR AF= 0.0291 (1139/39154). AF 95% confidence interval is 0.0277. There are 26 homozygotes in gnomad4. There are 682 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 26 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MASP1 | NM_001879.6 | c.1910-239_1910-238insG | intron_variant | ENST00000337774.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MASP1 | ENST00000337774.10 | c.1910-239_1910-238insG | intron_variant | 1 | NM_001879.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00943 AC: 1361AN: 144276Hom.: 26 Cov.: 30
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GnomAD4 genome ? AF: 0.00942 AC: 1360AN: 144360Hom.: 26 Cov.: 30 AF XY: 0.00973 AC XY: 682AN XY: 70124
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 14, 2019 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at