19-8977341-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001414686.1(MUC16):c.4344A>C(p.Lys1448Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 1,613,708 control chromosomes in the GnomAD database, including 408,039 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 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.3918A>C | p.Lys1306Asn | missense_variant | 4/93 | ENST00000711671.1 | |
MUC16 | NM_001414686.1 | c.4344A>C | p.Lys1448Asn | missense_variant | 5/94 | ||
MUC16 | NM_001414687.1 | c.3798A>C | p.Lys1266Asn | missense_variant | 1/90 | ||
MUC16 | NM_024690.2 | c.3798A>C | p.Lys1266Asn | missense_variant | 1/84 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC16 | ENST00000711672.1 | c.3918A>C | p.Lys1306Asn | missense_variant | 4/88 | A2 | |||
MUC16 | ENST00000710609.1 | c.3918A>C | p.Lys1306Asn | missense_variant | 4/87 | A2 | |||
MUC16 | ENST00000397910.8 | c.3798A>C | p.Lys1266Asn | missense_variant | 1/84 | 5 | P2 | ||
MUC16 | ENST00000710610.1 | c.302-7462A>C | intron_variant | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.772 AC: 117356AN: 151918Hom.: 45951 Cov.: 30
GnomAD3 exomes AF: 0.743 AC: 185321AN: 249274Hom.: 69581 AF XY: 0.739 AC XY: 99888AN XY: 135224
GnomAD4 exome AF: 0.701 AC: 1024741AN: 1461670Hom.: 362022 Cov.: 68 AF XY: 0.703 AC XY: 511149AN XY: 727112
GnomAD4 genome ? AF: 0.773 AC: 117484AN: 152038Hom.: 46017 Cov.: 30 AF XY: 0.777 AC XY: 57755AN XY: 74294
ClinVar
Submissions by phenotype
MUC16-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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