rs1046268
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001267560.2(TJP3):āc.2693T>Cā(p.Met898Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 1,605,634 control chromosomes in the GnomAD database, including 243,832 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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
NM_001267560.2 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 | UniProt |
---|---|---|---|---|---|---|---|
TJP3 | NM_001267560.2 | c.2693T>C | p.Met898Thr | missense_variant | 21/21 | ENST00000541714.7 | |
TJP3 | NM_001267561.2 | c.2720T>C | p.Met907Thr | missense_variant | 21/21 | ||
TJP3 | XM_047438611.1 | c.2891T>C | p.Met964Thr | missense_variant | 21/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TJP3 | ENST00000541714.7 | c.2693T>C | p.Met898Thr | missense_variant | 21/21 | 2 | NM_001267560.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.508 AC: 76964AN: 151580Hom.: 20461 Cov.: 31
GnomAD3 exomes AF: 0.569 AC: 136125AN: 239428Hom.: 39446 AF XY: 0.566 AC XY: 73288AN XY: 129530
GnomAD4 exome AF: 0.552 AC: 802147AN: 1453936Hom.: 223348 Cov.: 48 AF XY: 0.552 AC XY: 398620AN XY: 722690
GnomAD4 genome ? AF: 0.508 AC: 77043AN: 151698Hom.: 20484 Cov.: 31 AF XY: 0.512 AC XY: 37976AN XY: 74108
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at