chr19-8876542-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001414686.1(MUC16):c.42517C>A(p.Gln14173Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,612,852 control chromosomes in the GnomAD database, including 78,503 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001414686.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC16 | NM_001401501.2 | c.42091C>A | p.Gln14031Lys | missense_variant | 77/93 | ENST00000711671.1 | |
MUC16 | NM_001414686.1 | c.42517C>A | p.Gln14173Lys | missense_variant | 78/94 | ||
MUC16 | NM_001414687.1 | c.41971C>A | p.Gln13991Lys | missense_variant | 74/90 | ||
MUC16 | NM_024690.2 | c.41869C>A | p.Gln13957Lys | missense_variant | 68/84 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC16 | ENST00000711672.1 | c.42055C>A | p.Gln14019Lys | missense_variant | 72/88 | A2 |
Frequencies
GnomAD3 genomes AF: 0.363 AC: 55136AN: 151782Hom.: 11012 Cov.: 30
GnomAD3 exomes AF: 0.331 AC: 82294AN: 248778Hom.: 14705 AF XY: 0.336 AC XY: 45389AN XY: 134938
GnomAD4 exome AF: 0.295 AC: 431577AN: 1460952Hom.: 67469 Cov.: 54 AF XY: 0.301 AC XY: 218707AN XY: 726746
GnomAD4 genome AF: 0.363 AC: 55208AN: 151900Hom.: 11034 Cov.: 30 AF XY: 0.363 AC XY: 26957AN XY: 74246
ClinVar
Submissions by phenotype
MUC16-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at