chr5-139307308-A-AT
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_018834.6(MATR3):c.-103dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 1,470,646 control chromosomes in the GnomAD database, including 332,573 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.55 ( 25512 hom., cov: 0)
Exomes 𝑓: 0.67 ( 307061 hom. )
Consequence
MATR3
NM_018834.6 5_prime_UTR
NM_018834.6 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.822
Genes affected
MATR3 (HGNC:6912): (matrin 3) This gene encodes a nuclear matrix protein, which is proposed to stabilize certain messenger RNA species. Mutations of this gene are associated with distal myopathy 2, which often includes vocal cord and pharyngeal weakness. Alternatively spliced transcript variants, including read-through transcripts composed of the upstream small nucleolar RNA host gene 4 (non-protein coding) and matrin 3 gene sequence, have been identified. Pseudogenes of this gene are located on chromosomes 1 and X. [provided by RefSeq, Aug 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 5-139307308-A-AT is Benign according to our data. Variant chr5-139307308-A-AT is described in ClinVar as [Benign]. Clinvar id is 351117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MATR3 | NM_018834.6 | c.-103dup | 5_prime_UTR_variant | 2/15 | ENST00000394805.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MATR3 | ENST00000394805.8 | c.-103dup | 5_prime_UTR_variant | 2/15 | 1 | NM_018834.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.548 AC: 83158AN: 151704Hom.: 25500 Cov.: 0
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GnomAD4 exome AF: 0.674 AC: 888567AN: 1318824Hom.: 307061 Cov.: 36 AF XY: 0.675 AC XY: 436745AN XY: 647260
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GnomAD4 genome ? AF: 0.548 AC: 83208AN: 151822Hom.: 25512 Cov.: 0 AF XY: 0.542 AC XY: 40217AN XY: 74168
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Distal myopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 09, 2019 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at