GeneBe

rs376566294

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001879.6(MASP1):​c.1910-247_1910-236delAAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000783 in 127,766 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000078 ( 0 hom., cov: 22)

Consequence

MASP1
NM_001879.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.232

Publications

0 publications found
Variant links:
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]
MASP1 Gene-Disease associations (from GenCC):
  • 3MC syndrome 1
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), PanelApp Australia
  • 3MC syndrome
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001879.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MASP1
NM_001879.6
MANE Plus Clinical
c.1910-247_1910-236delAAAAAAAAAAAA
intron
N/ANP_001870.3

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MASP1
ENST00000337774.10
TSL:1 MANE Plus Clinical
c.1910-247_1910-236delAAAAAAAAAAAA
intron
N/AENSP00000336792.5P48740-1

Frequencies

GnomAD3 genomes
AF:
0.00000783
AC:
1
AN:
127766
Hom.:
0
Cov.:
22
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000156
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00000783
AC:
1
AN:
127766
Hom.:
0
Cov.:
22
AF XY:
0.0000164
AC XY:
1
AN XY:
60804
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
32692
American (AMR)
AF:
0.00
AC:
0
AN:
12012
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3214
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4282
South Asian (SAS)
AF:
0.00
AC:
0
AN:
3922
European-Finnish (FIN)
AF:
0.000156
AC:
1
AN:
6406
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
260
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
62400
Other (OTH)
AF:
0.00
AC:
0
AN:
1732
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs376566294; hg19: chr3-186938284; API