chr19-35904582-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_003332.4(TYROBP):c.329C>T(p.Pro110Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,398 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars). Synonymous variant affecting the same amino acid position (i.e. P110P) has been classified as Likely benign.
Frequency
Consequence
NM_003332.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TYROBP | NM_003332.4 | c.329C>T | p.Pro110Leu | missense_variant | 5/5 | ENST00000262629.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TYROBP | ENST00000262629.9 | c.329C>T | p.Pro110Leu | missense_variant | 5/5 | 1 | NM_003332.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151926Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250534Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135448
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461472Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726968
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151926Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74206
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at