chr19-1611746-T-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003200.5(TCF3):c.1926A>T(p.Pro642=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P642P) has been classified as Likely benign.
Frequency
Consequence
NM_003200.5 synonymous
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 |
---|---|---|---|---|---|---|---|
TCF3 | NM_003200.5 | c.1926A>T | p.Pro642= | synonymous_variant | 19/19 | ENST00000262965.12 | |
TCF3 | NM_001136139.4 | c.1917A>T | p.Pro639= | synonymous_variant | 19/20 | ENST00000588136.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCF3 | ENST00000262965.12 | c.1926A>T | p.Pro642= | synonymous_variant | 19/19 | 1 | NM_003200.5 | A1 | |
TCF3 | ENST00000588136.7 | c.1917A>T | p.Pro639= | synonymous_variant | 19/20 | 2 | NM_001136139.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151970Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250638Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135748
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151970Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74238
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at