chr19-1611703-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 10P and 2B. PVS1PM2BP6_Moderate
The NM_001136139.4(TCF3):c.*3+1G>A variant causes a splice donor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,738 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001136139.4 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCF3 | NM_001136139.4 | c.*3+1G>A | splice_donor_variant | ENST00000588136.7 | |||
TCF3 | NM_003200.5 | c.*4G>A | 3_prime_UTR_variant | 19/19 | ENST00000262965.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF3 | ENST00000588136.7 | c.*3+1G>A | splice_donor_variant | 2 | NM_001136139.4 | P3 | |||
TCF3 | ENST00000262965.12 | c.*4G>A | 3_prime_UTR_variant | 19/19 | 1 | NM_003200.5 | A1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459738Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726058
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
TCF3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 25, 2020 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.