11-1242546-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002458.3(MUC5B):c.5666C>T(p.Pro1889Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,613,674 control chromosomes in the GnomAD database, including 15,607 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 (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_002458.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.135 AC: 20495AN: 151938Hom.: 1525 Cov.: 32
GnomAD3 exomes AF: 0.151 AC: 37674AN: 249322Hom.: 3592 AF XY: 0.146 AC XY: 19787AN XY: 135214
GnomAD4 exome AF: 0.133 AC: 194389AN: 1461618Hom.: 14079 Cov.: 87 AF XY: 0.133 AC XY: 96952AN XY: 727100
GnomAD4 genome AF: 0.135 AC: 20509AN: 152056Hom.: 1528 Cov.: 32 AF XY: 0.141 AC XY: 10518AN XY: 74334
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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