rs2276176
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001080467.3(MYO5B):c.3276+11T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 1,613,030 control chromosomes in the GnomAD database, including 40,786 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.23 ( 4204 hom., cov: 32)
Exomes 𝑓: 0.22 ( 36582 hom. )
Consequence
MYO5B
NM_001080467.3 intron
NM_001080467.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0160
Genes affected
MYO5B (HGNC:7603): (myosin VB) The protein encoded by this gene, together with other proteins, may be involved in plasma membrane recycling. Mutations in this gene are associated with microvillous inclusion disease. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 18-49878934-A-G is Benign according to our data. Variant chr18-49878934-A-G is described in ClinVar as [Benign]. Clinvar id is 327030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-49878934-A-G is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO5B | NM_001080467.3 | c.3276+11T>C | intron_variant | ENST00000285039.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO5B | ENST00000285039.12 | c.3276+11T>C | intron_variant | 1 | NM_001080467.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.232 AC: 35133AN: 151574Hom.: 4200 Cov.: 32
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GnomAD3 exomes AF: 0.253 AC: 62941AN: 249086Hom.: 8666 AF XY: 0.254 AC XY: 34306AN XY: 135168
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GnomAD4 exome AF: 0.217 AC: 317246AN: 1461338Hom.: 36582 Cov.: 34 AF XY: 0.220 AC XY: 160194AN XY: 726998
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GnomAD4 genome ? AF: 0.232 AC: 35168AN: 151692Hom.: 4204 Cov.: 32 AF XY: 0.238 AC XY: 17630AN XY: 74120
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Congenital microvillous atrophy Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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