rs4679392
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000616727.4(MUC13):āc.299T>Cā(p.Ile100Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 1,612,616 control chromosomes in the GnomAD database, including 148,363 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000616727.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MUC13 | NM_033049.4 | c.299T>C | p.Ile100Thr | missense_variant | 2/12 | ENST00000616727.4 | NP_149038.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MUC13 | ENST00000616727.4 | c.299T>C | p.Ile100Thr | missense_variant | 2/12 | 1 | NM_033049.4 | ENSP00000485028 | P1 | |
MUC13 | ENST00000478191.1 | c.53-147T>C | intron_variant | 4 | ENSP00000418660 | |||||
MUC13 | ENST00000490147.1 | n.25T>C | non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.431 AC: 65398AN: 151654Hom.: 14109 Cov.: 32
GnomAD3 exomes AF: 0.426 AC: 106577AN: 250278Hom.: 23276 AF XY: 0.429 AC XY: 58082AN XY: 135460
GnomAD4 exome AF: 0.426 AC: 622386AN: 1460844Hom.: 134242 Cov.: 49 AF XY: 0.428 AC XY: 310734AN XY: 726762
GnomAD4 genome AF: 0.431 AC: 65461AN: 151772Hom.: 14121 Cov.: 32 AF XY: 0.434 AC XY: 32217AN XY: 74168
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at