rs184565965
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002458.3(MUC5B):āc.9179A>Cā(p.Lys3060Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0255 in 149,550 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_002458.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC5B | NM_002458.3 | c.9179A>C | p.Lys3060Thr | missense_variant | 31/49 | ENST00000529681.5 | |
MUC5B-AS1 | NR_157183.1 | n.57-3421T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC5B | ENST00000529681.5 | c.9179A>C | p.Lys3060Thr | missense_variant | 31/49 | 5 | NM_002458.3 | P1 | |
MUC5B-AS1 | ENST00000532061.2 | n.57-3421T>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0255 AC: 3817AN: 149424Hom.: 79 Cov.: 29
GnomAD3 exomes AF: 0.0267 AC: 6658AN: 249046Hom.: 154 AF XY: 0.0265 AC XY: 3585AN XY: 135150
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0302 AC: 44130AN: 1461448Hom.: 923 Cov.: 76 AF XY: 0.0295 AC XY: 21482AN XY: 727004
GnomAD4 genome AF: 0.0255 AC: 3816AN: 149550Hom.: 79 Cov.: 29 AF XY: 0.0260 AC XY: 1899AN XY: 72984
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 | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at