chr4-6576760-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015274.3(MAN2B2):c.285+36A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 1,607,672 control chromosomes in the GnomAD database, including 559,059 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.82 ( 50862 hom., cov: 33)
Exomes 𝑓: 0.84 ( 508197 hom. )
Consequence
MAN2B2
NM_015274.3 intron
NM_015274.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.28
Genes affected
MAN2B2 (HGNC:29623): (mannosidase alpha class 2B member 2) Predicted to enable alpha-mannosidase activity. Predicted to be involved in mannose metabolic process. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.98).
BP6
Variant 4-6576760-A-G is Benign according to our data. Variant chr4-6576760-A-G is described in ClinVar as [Benign]. Clinvar id is 2688204.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN2B2 | NM_015274.3 | c.285+36A>G | intron_variant | ENST00000285599.8 | |||
MAN2B2 | NM_001292038.2 | c.285+36A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN2B2 | ENST00000285599.8 | c.285+36A>G | intron_variant | 1 | NM_015274.3 | P1 | |||
MAN2B2 | ENST00000504248.5 | c.285+36A>G | intron_variant | 2 | |||||
MAN2B2 | ENST00000505907.1 | c.281+36A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.816 AC: 124056AN: 152016Hom.: 50815 Cov.: 33
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GnomAD3 exomes AF: 0.839 AC: 209401AN: 249528Hom.: 88083 AF XY: 0.840 AC XY: 113490AN XY: 135112
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GnomAD4 exome AF: 0.835 AC: 1215564AN: 1455538Hom.: 508197 Cov.: 38 AF XY: 0.835 AC XY: 603732AN XY: 722914
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GnomAD4 genome AF: 0.816 AC: 124163AN: 152134Hom.: 50862 Cov.: 33 AF XY: 0.816 AC XY: 60652AN XY: 74358
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 99% of patients studied by a panel of primary immunodeficiencies. Number of patients: 94. Only high quality variants are reported. - |
Computational scores
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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