rs17433672
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000355460.6(MBNL1):c.-1409C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0619 in 310,936 control chromosomes in the GnomAD database, including 841 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.059 ( 385 hom., cov: 32)
Exomes 𝑓: 0.065 ( 456 hom. )
Consequence
MBNL1
ENST00000355460.6 5_prime_UTR
ENST00000355460.6 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.41
Genes affected
MBNL1 (HGNC:6923): (muscleblind like splicing regulator 1) This gene encodes a member of the muscleblind protein family which was initially described in Drosophila melanogaster. The encoded protein is a C3H-type zinc finger protein that modulates alternative splicing of pre-mRNAs. Muscleblind proteins bind specifically to expanded dsCUG RNA but not to normal size CUG repeats and may thereby play a role in the pathophysiology of myotonic dystrophy. Mice lacking this gene exhibited muscle abnormalities and cataracts. Several alternatively spliced transcript variants have been described but the full-length natures of only some have been determined. The different isoforms are thought to have different binding specificities and/or splicing activities. [provided by RefSeq, Sep 2015]
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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=-0.73).
BP6
?
Variant 3-152268473-C-T is Benign according to our data. Variant chr3-152268473-C-T is described in ClinVar as [Benign]. Clinvar id is 218788.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.084 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBNL1-AS1 | NR_027037.1 | n.788G>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBNL1 | ENST00000355460.6 | c.-1409C>T | 5_prime_UTR_variant | 1/9 | 1 | A1 | |||
MBNL1 | ENST00000282486.10 | c.-1409C>T | 5_prime_UTR_variant | 1/10 | 5 | P4 | |||
MBNL1 | ENST00000282488.11 | c.-1409C>T | 5_prime_UTR_variant | 1/11 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0587 AC: 8931AN: 152194Hom.: 385 Cov.: 32
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GnomAD4 exome AF: 0.0650 AC: 10310AN: 158624Hom.: 456 Cov.: 0 AF XY: 0.0586 AC XY: 5120AN XY: 87374
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GnomAD4 genome ? AF: 0.0587 AC: 8934AN: 152312Hom.: 385 Cov.: 32 AF XY: 0.0591 AC XY: 4400AN XY: 74484
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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 | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Jul 10, 2015 | - - |
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