rs11602663
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005961.3(MUC6):c.3590-44G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,602,844 control chromosomes in the GnomAD database, including 25,988 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 0.13 ( 1696 hom., cov: 33)
Exomes 𝑓: 0.18 ( 24292 hom. )
Consequence
MUC6
NM_005961.3 intron
NM_005961.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.647
Genes affected
MUC6 (HGNC:7517): (mucin 6, 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. [provided by RefSeq, Dec 2016]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC6 | NM_005961.3 | c.3590-44G>A | intron_variant | ENST00000421673.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC6 | ENST00000421673.7 | c.3590-44G>A | intron_variant | 5 | NM_005961.3 | P1 | |||
MUC6 | ENST00000527242.2 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.134 AC: 20380AN: 152056Hom.: 1691 Cov.: 33
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GnomAD3 exomes AF: 0.146 AC: 35209AN: 241890Hom.: 3095 AF XY: 0.149 AC XY: 19644AN XY: 131540
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GnomAD4 exome AF: 0.176 AC: 255785AN: 1450670Hom.: 24292 Cov.: 34 AF XY: 0.175 AC XY: 126061AN XY: 720938
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GnomAD4 genome ? AF: 0.134 AC: 20392AN: 152174Hom.: 1696 Cov.: 33 AF XY: 0.132 AC XY: 9828AN XY: 74384
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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