11-1250996-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_002458.3(MUC5B):c.14116A>T(p.Thr4706Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000438 in 1,596,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T4706P) has been classified as Benign.
Frequency
Consequence
NM_002458.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC5B | NM_002458.3 | c.14116A>T | p.Thr4706Ser | missense_variant | 31/49 | ENST00000529681.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC5B | ENST00000529681.5 | c.14116A>T | p.Thr4706Ser | missense_variant | 31/49 | 5 | NM_002458.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000673 AC: 1AN: 148616Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246148Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133722
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1448082Hom.: 0 Cov.: 109 AF XY: 0.00000139 AC XY: 1AN XY: 720560
GnomAD4 genome ? AF: 0.00000672 AC: 1AN: 148738Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 1AN XY: 72580
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at