rs12732
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_033049.4(MUC13):c.*1022T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,962 control chromosomes in the GnomAD database, including 2,337 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.17 ( 2327 hom., cov: 32)
Exomes 𝑓: 0.16 ( 10 hom. )
Consequence
MUC13
NM_033049.4 3_prime_UTR
NM_033049.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.552
Genes affected
MUC13 (HGNC:7511): (mucin 13, cell surface associated) Epithelial mucins, such as MUC13, are a family of secreted and cell surface glycoproteins expressed by ductal and glandular epithelial tissues (Williams et al., 2001 [PubMed 11278439]).[supplied by OMIM, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC13 | NM_033049.4 | c.*1022T>C | 3_prime_UTR_variant | 12/12 | ENST00000616727.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC13 | ENST00000616727.4 | c.*1022T>C | 3_prime_UTR_variant | 12/12 | 1 | NM_033049.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.166 AC: 25265AN: 152014Hom.: 2324 Cov.: 32
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GnomAD4 exome AF: 0.157 AC: 130AN: 830Hom.: 10 Cov.: 0 AF XY: 0.158 AC XY: 66AN XY: 418
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GnomAD4 genome ? AF: 0.166 AC: 25275AN: 152132Hom.: 2327 Cov.: 32 AF XY: 0.164 AC XY: 12211AN XY: 74374
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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