rs199852211
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_004817.4(TJP2):c.2819C>T(p.Pro940Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000199 in 1,613,240 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004817.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TJP2 | ENST00000377245.9 | c.2819C>T | p.Pro940Leu | missense_variant | Exon 19 of 23 | 1 | NM_004817.4 | ENSP00000366453.4 | ||
ENSG00000285130 | ENST00000642889.1 | c.3206C>T | p.Pro1069Leu | missense_variant | Exon 21 of 25 | ENSP00000493780.1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000375 AC: 93AN: 247682Hom.: 1 AF XY: 0.000476 AC XY: 64AN XY: 134386
GnomAD4 exome AF: 0.000208 AC: 304AN: 1460912Hom.: 1 Cov.: 32 AF XY: 0.000310 AC XY: 225AN XY: 726756
GnomAD4 genome AF: 0.000112 AC: 17AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74482
ClinVar
Submissions by phenotype
not specified Benign:1
p.Pro940Leu in exon 19 of TJP2: This variant is not expected to have clinical si gnificance because it has been identified in 0.4% (60/15540) of South Asian chro mosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.or g; dbSNP rs199852211). -
TJP2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at