chr19-8871627-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001414686.1(MUC16):c.42620G>A(p.Arg14207Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00144 in 1,588,182 control chromosomes in the GnomAD database, including 17 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
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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 |
---|---|---|---|---|---|---|---|
MUC16 | NM_001401501.2 | c.42194G>A | p.Arg14065Gln | missense_variant | 79/93 | ENST00000711671.1 | |
MUC16 | NM_001414686.1 | c.42620G>A | p.Arg14207Gln | missense_variant | 80/94 | ||
MUC16 | NM_001414687.1 | c.42074G>A | p.Arg14025Gln | missense_variant | 76/90 | ||
MUC16 | NM_024690.2 | c.41972G>A | p.Arg13991Gln | missense_variant | 70/84 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC16 | ENST00000711672.1 | c.42158G>A | p.Arg14053Gln | missense_variant | 74/88 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00420 AC: 638AN: 152056Hom.: 3 Cov.: 31
GnomAD3 exomes AF: 0.00228 AC: 511AN: 224610Hom.: 7 AF XY: 0.00238 AC XY: 290AN XY: 121894
GnomAD4 exome AF: 0.00115 AC: 1649AN: 1436008Hom.: 14 Cov.: 32 AF XY: 0.00127 AC XY: 909AN XY: 713570
GnomAD4 genome ? AF: 0.00419 AC: 637AN: 152174Hom.: 3 Cov.: 31 AF XY: 0.00415 AC XY: 309AN XY: 74414
ClinVar
Submissions by phenotype
MUC16-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 14, 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