rs3737612
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006610.4(MASP2):c.741+44C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000202 in 1,535,140 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00027 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00019 ( 1 hom. )
Consequence
MASP2
NM_006610.4 intron
NM_006610.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0680
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MASP2 | NM_006610.4 | c.741+44C>T | intron_variant | ENST00000400897.8 | |||
MASP2 | XM_017000097.1 | c.741+44C>T | intron_variant | ||||
MASP2 | XM_047439758.1 | c.545-273C>T | intron_variant | ||||
MASP2 | XR_001736931.1 | n.773+44C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MASP2 | ENST00000400897.8 | c.741+44C>T | intron_variant | 1 | NM_006610.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000269 AC: 41AN: 152174Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000664 AC: 124AN: 186822Hom.: 0 AF XY: 0.000631 AC XY: 63AN XY: 99838
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GnomAD4 exome AF: 0.000195 AC: 269AN: 1382848Hom.: 1 Cov.: 24 AF XY: 0.000184 AC XY: 126AN XY: 684596
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GnomAD4 genome ? AF: 0.000269 AC: 41AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74474
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ClinVar
Not reported inComputational scores
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Name
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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