rs4713419
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001395414.1(MUC22):c.71-43A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,450,282 control chromosomes in the GnomAD database, including 14,240 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 0.12 ( 1383 hom., cov: 32)
Exomes 𝑓: 0.14 ( 12857 hom. )
Consequence
MUC22
NM_001395414.1 intron
NM_001395414.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.121
Genes affected
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC22 | NM_001395414.1 | c.71-43A>G | intron_variant | ENST00000561890.1 | |||
MUC22 | NM_001198815.1 | c.71-43A>G | intron_variant | ||||
MUC22 | NM_001318484.1 | c.80-43A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC22 | ENST00000561890.1 | c.71-43A>G | intron_variant | 2 | NM_001395414.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.124 AC: 18834AN: 151934Hom.: 1385 Cov.: 32
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GnomAD3 exomes AF: 0.154 AC: 9097AN: 58988Hom.: 900 AF XY: 0.155 AC XY: 4709AN XY: 30358
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GnomAD4 exome AF: 0.136 AC: 177144AN: 1298228Hom.: 12857 Cov.: 30 AF XY: 0.137 AC XY: 86519AN XY: 632380
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GnomAD4 genome ? AF: 0.124 AC: 18826AN: 152054Hom.: 1383 Cov.: 32 AF XY: 0.126 AC XY: 9369AN XY: 74330
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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
La Branchor
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