chr19-8863312-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001414686.1(MUC16):c.43331G>A(p.Arg14444Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00323 in 1,605,806 control chromosomes in the GnomAD database, including 15 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 Likely benign (★★).
Frequency
Consequence
NM_001414686.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC16 | NM_001401501.2 | c.42905G>A | p.Arg14302Lys | missense_variant | 85/93 | ENST00000711671.1 | |
MUC16 | NM_001414686.1 | c.43331G>A | p.Arg14444Lys | missense_variant | 86/94 | ||
MUC16 | NM_001414687.1 | c.42785G>A | p.Arg14262Lys | missense_variant | 82/90 | ||
MUC16 | NM_024690.2 | c.42683G>A | p.Arg14228Lys | missense_variant | 76/84 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC16 | ENST00000711672.1 | c.42869G>A | p.Arg14290Lys | missense_variant | 80/88 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00294 AC: 447AN: 152084Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00320 AC: 753AN: 235578Hom.: 3 AF XY: 0.00300 AC XY: 381AN XY: 127182
GnomAD4 exome AF: 0.00326 AC: 4732AN: 1453604Hom.: 12 Cov.: 32 AF XY: 0.00310 AC XY: 2236AN XY: 721990
GnomAD4 genome ? AF: 0.00294 AC: 447AN: 152202Hom.: 3 Cov.: 32 AF XY: 0.00335 AC XY: 249AN XY: 74410
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | MUC16: BP4, BS2 - |
MUC16-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 10, 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