rs930509
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001378373.1(MBL2):c.374-83G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 1,005,892 control chromosomes in the GnomAD database, including 326,851 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 0.84 ( 53499 hom., cov: 33)
Exomes 𝑓: 0.80 ( 273352 hom. )
Consequence
MBL2
NM_001378373.1 intron
NM_001378373.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.793
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBL2 | NM_001378373.1 | c.374-83G>C | intron_variant | ENST00000674931.1 | |||
MBL2 | NM_000242.3 | c.374-83G>C | intron_variant | ||||
MBL2 | NM_001378374.1 | c.374-83G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBL2 | ENST00000674931.1 | c.374-83G>C | intron_variant | NM_001378373.1 | P1 | ||||
MBL2 | ENST00000373968.3 | c.374-83G>C | intron_variant | 1 | P1 | ||||
MBL2 | ENST00000675947.1 | c.374-83G>C | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.838 AC: 127201AN: 151868Hom.: 53444 Cov.: 33
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GnomAD4 exome AF: 0.799 AC: 682290AN: 853906Hom.: 273352 AF XY: 0.798 AC XY: 343790AN XY: 431000
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GnomAD4 genome ? AF: 0.838 AC: 127316AN: 151986Hom.: 53499 Cov.: 33 AF XY: 0.838 AC XY: 62229AN XY: 74294
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ClinVar
Not reported inComputational 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