11-1242438-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002458.3(MUC5B):c.5558C>T(p.Thr1853Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,782 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002458.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249108Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135144
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461602Hom.: 0 Cov.: 68 AF XY: 0.00000413 AC XY: 3AN XY: 727088
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74406
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5558C>T (p.T1853M) alteration is located in exon 31 (coding exon 31) of the MUC5B gene. This alteration results from a C to T substitution at nucleotide position 5558, causing the threonine (T) at amino acid position 1853 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at