rs7103978
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_002457.5(MUC2):āc.3600A>Gā(p.Ala1200=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0878 in 1,611,516 control chromosomes in the GnomAD database, including 6,612 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: š 0.079 ( 512 hom., cov: 34)
Exomes š: 0.089 ( 6100 hom. )
Consequence
MUC2
NM_002457.5 synonymous
NM_002457.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.37
Genes affected
MUC2 (HGNC:7512): (mucin 2, oligomeric mucus/gel-forming) This gene encodes a member of the mucin protein family. Mucins are high molecular weight glycoproteins produced by many epithelial tissues. The protein encoded by this gene is secreted and forms an insoluble mucous barrier that protects the gut lumen. The protein polymerizes into a gel of which 80% is composed of oligosaccharide side chains by weight. The protein features a central domain containing tandem repeats rich in threonine and proline that varies between 50 and 115 copies in different individuals. Downregulation of this gene has been observed in patients with Crohn disease and ulcerative colitis. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP7
?
Synonymous conserved (PhyloP=-1.37 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0933 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC2 | NM_002457.5 | c.3600A>G | p.Ala1200= | synonymous_variant | 26/58 | ENST00000713550.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC2 | ENST00000675028.1 | c.3600A>G | p.Ala1200= | synonymous_variant | 26/30 | P3 | |||
MUC2 | ENST00000361558.7 | n.3627A>G | non_coding_transcript_exon_variant | 26/49 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0786 AC: 11962AN: 152100Hom.: 509 Cov.: 34
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GnomAD3 exomes AF: 0.0754 AC: 18488AN: 245298Hom.: 784 AF XY: 0.0753 AC XY: 10056AN XY: 133536
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GnomAD4 exome AF: 0.0888 AC: 129548AN: 1459298Hom.: 6100 Cov.: 33 AF XY: 0.0877 AC XY: 63666AN XY: 725746
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GnomAD4 genome ? AF: 0.0787 AC: 11981AN: 152218Hom.: 512 Cov.: 34 AF XY: 0.0784 AC XY: 5837AN XY: 74418
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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