rs555879
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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.*308C>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 0.54 in 366,126 control chromosomes in the GnomAD database, including 53,808 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.54 ( 22089 hom., cov: 33)
Exomes 𝑓: 0.54 ( 31719 hom. )
Consequence
MYO5B
NM_001080467.3 3_prime_UTR
NM_001080467.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.246
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=-0.89).
BP6
?
Variant 18-49826163-G-A is Benign according to our data. Variant chr18-49826163-G-A is described in ClinVar as [Benign]. Clinvar id is 326990.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO5B | NM_001080467.3 | c.*308C>T | 3_prime_UTR_variant | 40/40 | ENST00000285039.12 | ||
SNHG22 | NR_117096.1 | n.40+12101G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO5B | ENST00000285039.12 | c.*308C>T | 3_prime_UTR_variant | 40/40 | 1 | NM_001080467.3 | P1 | ||
SNHG22 | ENST00000589499.1 | n.40+12101G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.538 AC: 81647AN: 151884Hom.: 22074 Cov.: 33
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GnomAD4 exome AF: 0.541 AC: 115827AN: 214124Hom.: 31719 Cov.: 2 AF XY: 0.542 AC XY: 62313AN XY: 114920
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GnomAD4 genome ? AF: 0.538 AC: 81711AN: 152002Hom.: 22089 Cov.: 33 AF XY: 0.538 AC XY: 39936AN XY: 74276
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Congenital microvillous atrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
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Name
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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