rs200226020
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_002458.3(MUC5B):c.3926C>T(p.Thr1309Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000239 in 1,610,002 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002458.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC5B | NM_002458.3 | c.3926C>T | p.Thr1309Met | missense_variant | 30/49 | ENST00000529681.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC5B | ENST00000529681.5 | c.3926C>T | p.Thr1309Met | missense_variant | 30/49 | 5 | NM_002458.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000342 AC: 52AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000541 AC: 134AN: 247510Hom.: 0 AF XY: 0.000469 AC XY: 63AN XY: 134320
GnomAD4 exome AF: 0.000224 AC: 326AN: 1457704Hom.: 1 Cov.: 33 AF XY: 0.000214 AC XY: 155AN XY: 724468
GnomAD4 genome ? AF: 0.000387 AC: 59AN: 152298Hom.: 1 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74466
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 20, 2017 | p.Thr1309Met in exon 30 of MUC5B: This variant is not expected to have clinical significance because it is not located within the splice consensus sequence. It has been identified in 0.5% (40/8608) of East Asian chromosomes by the Exome Ag gregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs200226020). - |
Interstitial lung disease 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 02, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at