chr19-8871595-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001414686.1(MUC16):c.42652C>T(p.Leu14218Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00804 in 1,608,972 control chromosomes in the GnomAD database, including 431 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 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.42226C>T | p.Leu14076Phe | missense_variant | 79/93 | ENST00000711671.1 | |
MUC16 | NM_001414686.1 | c.42652C>T | p.Leu14218Phe | missense_variant | 80/94 | ||
MUC16 | NM_001414687.1 | c.42106C>T | p.Leu14036Phe | missense_variant | 76/90 | ||
MUC16 | NM_024690.2 | c.42004C>T | p.Leu14002Phe | missense_variant | 70/84 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC16 | ENST00000711672.1 | c.42190C>T | p.Leu14064Phe | missense_variant | 74/88 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0103 AC: 1565AN: 152092Hom.: 55 Cov.: 31
GnomAD3 exomes AF: 0.0225 AC: 5485AN: 243608Hom.: 198 AF XY: 0.0213 AC XY: 2810AN XY: 132196
GnomAD4 exome AF: 0.00780 AC: 11362AN: 1456762Hom.: 376 Cov.: 32 AF XY: 0.00875 AC XY: 6342AN XY: 724610
GnomAD4 genome AF: 0.0103 AC: 1569AN: 152210Hom.: 55 Cov.: 31 AF XY: 0.0121 AC XY: 900AN XY: 74424
ClinVar
Submissions by phenotype
MUC16-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 03, 2020 | 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