15-29710947-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001330239.4(TJP1):c.4256A>G(p.Tyr1419Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,614,148 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001330239.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TJP1 | NM_001330239.4 | c.4256A>G | p.Tyr1419Cys | missense_variant | 24/28 | ENST00000614355.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TJP1 | ENST00000614355.5 | c.4256A>G | p.Tyr1419Cys | missense_variant | 24/28 | 5 | NM_001330239.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249310Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135256
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461828Hom.: 1 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727204
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2022 | The c.4256A>G (p.Y1419C) alteration is located in exon 24 (coding exon 24) of the TJP1 gene. This alteration results from a A to G substitution at nucleotide position 4256, causing the tyrosine (Y) at amino acid position 1419 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at