rs78692183
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002458.3(MUC5B):āc.5647A>Gā(p.Ser1883Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0297 in 1,613,698 control chromosomes in the GnomAD database, including 913 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 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.5647A>G | p.Ser1883Gly | missense_variant | 31/49 | ENST00000529681.5 | |
MUC5B-AS1 | NR_157183.1 | n.168T>C | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC5B | ENST00000529681.5 | c.5647A>G | p.Ser1883Gly | missense_variant | 31/49 | 5 | NM_002458.3 | P1 | |
MUC5B-AS1 | ENST00000532061.2 | n.168T>C | non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0251 AC: 3822AN: 151968Hom.: 63 Cov.: 32
GnomAD3 exomes AF: 0.0268 AC: 6680AN: 249352Hom.: 144 AF XY: 0.0266 AC XY: 3592AN XY: 135206
GnomAD4 exome AF: 0.0302 AC: 44149AN: 1461612Hom.: 850 Cov.: 81 AF XY: 0.0295 AC XY: 21483AN XY: 727088
GnomAD4 genome ? AF: 0.0251 AC: 3823AN: 152086Hom.: 63 Cov.: 32 AF XY: 0.0255 AC XY: 1898AN XY: 74340
ClinVar
Submissions by phenotype
not specified Benign:1
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