rs4729656
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001040105.2(MUC17):c.*285T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 283,884 control chromosomes in the GnomAD database, including 56,100 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 0.62 ( 29676 hom., cov: 32)
Exomes 𝑓: 0.63 ( 26424 hom. )
Consequence
MUC17
NM_001040105.2 3_prime_UTR
NM_001040105.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.75
Genes affected
MUC17 (HGNC:16800): (mucin 17, cell surface associated) The protein encoded by this gene is a membrane-bound mucin that provides protection to gut epithelial cells. The encoded protein contains about 60 tandem repeats, with each repeat being around 60 aa. N-glycosylation enables the encoded protein to localize on the cell surface, while the C-terminus interacts with the scaffold protein PDZ domain containing 1 (PDZK1). Two transcript variants, one protein-coding and the other non-protein coding, have been found for this gene. [provided by RefSeq, Nov 2015]
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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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC17 | NM_001040105.2 | c.*285T>A | 3_prime_UTR_variant | 13/13 | ENST00000306151.9 | ||
MUC17 | NR_133665.2 | n.13670T>A | non_coding_transcript_exon_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC17 | ENST00000306151.9 | c.*285T>A | 3_prime_UTR_variant | 13/13 | 1 | NM_001040105.2 | P1 | ||
RN7SKP54 | ENST00000410704.1 | n.31T>A | non_coding_transcript_exon_variant | 1/1 | |||||
MUC17 | ENST00000379439.3 | c.*826T>A | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 1 |
Frequencies
GnomAD3 genomes AF: 0.621 AC: 94329AN: 151978Hom.: 29653 Cov.: 32
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GnomAD4 exome AF: 0.631 AC: 83124AN: 131788Hom.: 26424 Cov.: 2 AF XY: 0.631 AC XY: 42754AN XY: 67764
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GnomAD4 genome AF: 0.621 AC: 94394AN: 152096Hom.: 29676 Cov.: 32 AF XY: 0.616 AC XY: 45781AN XY: 74344
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at