rs7095891
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001378373.1(MBL2):c.-9-57C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 1,535,498 control chromosomes in the GnomAD database, including 46,114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.29 ( 7902 hom., cov: 33)
Exomes 𝑓: 0.23 ( 38212 hom. )
Consequence
MBL2
NM_001378373.1 intron
NM_001378373.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.511
Genes affected
MBL2 (HGNC:6922): (mannose binding lectin 2) This gene encodes the soluble mannose-binding lectin or mannose-binding protein found in serum. The protein encoded belongs to the collectin family and is an important element in the innate immune system. The protein recognizes and binds to mannose and N-acetylglucosamine on many microorganisms, including bacteria, yeast, and viruses including influenza virus, HIV and SARS-CoV. This binding activates the classical complement pathway. Deficiencies of this gene have been associated with susceptibility to autoimmune and infectious diseases. [provided by RefSeq, Jun 2020]
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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=-0.9).
BP6
?
Variant 10-52771701-G-A is Benign according to our data. Variant chr10-52771701-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 368900.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBL2 | NM_001378373.1 | c.-9-57C>T | intron_variant | ENST00000674931.1 | |||
MBL2 | NM_001378374.1 | c.-24-42C>T | intron_variant | ||||
MBL2 | NM_000242.3 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBL2 | ENST00000674931.1 | c.-9-57C>T | intron_variant | NM_001378373.1 | P1 | ||||
MBL2 | ENST00000675947.1 | c.-24-42C>T | intron_variant | P1 | |||||
MBL2 | ENST00000373968.3 | upstream_gene_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.293 AC: 44503AN: 151986Hom.: 7889 Cov.: 33
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GnomAD4 exome AF: 0.228 AC: 315227AN: 1383394Hom.: 38212 Cov.: 32 AF XY: 0.228 AC XY: 154684AN XY: 679392
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GnomAD4 genome ? AF: 0.293 AC: 44549AN: 152104Hom.: 7902 Cov.: 33 AF XY: 0.288 AC XY: 21441AN XY: 74356
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Mannose-binding lectin deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at