19-8862883-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001414686.1(MUC16):c.43405A>G(p.Thr14469Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,604,718 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/17 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.42979A>G | p.Thr14327Ala | missense_variant | 86/93 | ENST00000711671.1 | |
MUC16 | NM_001414686.1 | c.43405A>G | p.Thr14469Ala | missense_variant | 87/94 | ||
MUC16 | NM_001414687.1 | c.42859A>G | p.Thr14287Ala | missense_variant | 83/90 | ||
MUC16 | NM_024690.2 | c.42757A>G | p.Thr14253Ala | missense_variant | 77/84 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC16 | ENST00000711672.1 | c.42943A>G | p.Thr14315Ala | missense_variant | 81/88 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00540 AC: 821AN: 152114Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00240 AC: 563AN: 234794Hom.: 1 AF XY: 0.00227 AC XY: 288AN XY: 126724
GnomAD4 exome AF: 0.000982 AC: 1427AN: 1452486Hom.: 7 Cov.: 31 AF XY: 0.00104 AC XY: 753AN XY: 721378
GnomAD4 genome ? AF: 0.00543 AC: 827AN: 152232Hom.: 10 Cov.: 32 AF XY: 0.00533 AC XY: 397AN XY: 74418
ClinVar
Submissions by phenotype
MUC16-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 25, 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