11-1090879-A-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_002457.5(MUC2):c.3600A>T(p.Ala1200=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,611,840 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
Consequence
NM_002457.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC2 | NM_002457.5 | c.3600A>T | 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>T | p.Ala1200= | synonymous_variant | 26/30 | P3 | |||
MUC2 | ENST00000361558.7 | n.3627A>T | non_coding_transcript_exon_variant | 26/49 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152116Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000204 AC: 5AN: 245298Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133536
GnomAD4 exome AF: 0.00000959 AC: 14AN: 1459724Hom.: 0 Cov.: 33 AF XY: 0.00000689 AC XY: 5AN XY: 725948
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152116Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74300
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at