rs56310773
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002458.3(MUC5B):c.16137-7C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 1,555,898 control chromosomes in the GnomAD database, including 859 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002458.3 splice_region, splice_polypyrimidine_tract, intron
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.16137-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000529681.5 | |||
MIR6744 | NR_106802.1 | n.60C>T | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC5B | ENST00000529681.5 | c.16137-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_002458.3 | P1 | |||
MIR6744 | ENST00000619480.1 | n.60C>T | mature_miRNA_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0250 AC: 3791AN: 151720Hom.: 63 Cov.: 31
GnomAD3 exomes AF: 0.0253 AC: 4211AN: 166686Hom.: 88 AF XY: 0.0247 AC XY: 2215AN XY: 89758
GnomAD4 exome AF: 0.0301 AC: 42234AN: 1404060Hom.: 796 Cov.: 30 AF XY: 0.0294 AC XY: 20390AN XY: 694028
GnomAD4 genome ? AF: 0.0250 AC: 3790AN: 151838Hom.: 63 Cov.: 31 AF XY: 0.0254 AC XY: 1885AN XY: 74198
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 21, 2013 | 16137-7C>T in intron 38 of MUC5B: This variant is not expected to have clinical significance because it has been identified in 3.0% (252/8296) of European Ameri can chromosomes from a broad population by the NHLBI Exome Sequencing Project (h ttp://evs.gs.washington.edu/EVS; dbSNP rs56310773). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at