rs2165813
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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.*1913C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,976 control chromosomes in the GnomAD database, including 6,768 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.28 ( 6768 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
MBL2
NM_001378373.1 3_prime_UTR
NM_001378373.1 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.399
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=-0.94).
BP6
?
Variant 10-52766224-G-A is Benign according to our data. Variant chr10-52766224-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 300117.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBL2 | NM_001378373.1 | c.*1913C>T | 3_prime_UTR_variant | 5/5 | ENST00000674931.1 | ||
MBL2 | NM_000242.3 | c.*1913C>T | 3_prime_UTR_variant | 4/4 | |||
MBL2 | NM_001378374.1 | c.*1913C>T | 3_prime_UTR_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBL2 | ENST00000674931.1 | c.*1913C>T | 3_prime_UTR_variant | 5/5 | NM_001378373.1 | P1 | |||
MBL2 | ENST00000373968.3 | c.*1913C>T | 3_prime_UTR_variant | 4/4 | 1 | P1 | |||
MBL2 | ENST00000675947.1 | c.*1913C>T | 3_prime_UTR_variant | 5/5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.283 AC: 43016AN: 151858Hom.: 6755 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
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GnomAD4 genome ? AF: 0.283 AC: 43069AN: 151976Hom.: 6768 Cov.: 32 AF XY: 0.281 AC XY: 20885AN XY: 74296
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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 | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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