18-49929610-GAAAAAAA-GAAAA
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS1
The NM_001080467.3(MYO5B):c.2004-15_2004-13delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00436 in 1,260,590 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000060 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0049 ( 0 hom. )
Consequence
MYO5B
NM_001080467.3 intron
NM_001080467.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.06
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00487 (5489/1127764) while in subpopulation AMR AF= 0.00723 (227/31410). AF 95% confidence interval is 0.00646. There are 0 homozygotes in gnomad4_exome. There are 2565 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO5B | ENST00000285039.12 | c.2004-15_2004-13delTTT | intron_variant | Intron 16 of 39 | 1 | NM_001080467.3 | ENSP00000285039.6 | |||
MYO5B | ENST00000697219.1 | c.1800-15_1800-13delTTT | intron_variant | Intron 14 of 37 | ENSP00000513188.1 |
Frequencies
GnomAD3 genomes AF: 0.0000602 AC: 8AN: 132848Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.00734 AC: 840AN: 114366Hom.: 0 AF XY: 0.00712 AC XY: 439AN XY: 61680
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GnomAD4 exome AF: 0.00487 AC: 5489AN: 1127764Hom.: 0 AF XY: 0.00455 AC XY: 2565AN XY: 563876
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GnomAD4 genome AF: 0.0000602 AC: 8AN: 132826Hom.: 0 Cov.: 0 AF XY: 0.0000630 AC XY: 4AN XY: 63444
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ClinVar
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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