19-1611732-G-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_003200.5(TCF3):āc.1940C>Gā(p.Ala647Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000477 in 1,613,546 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003200.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TCF3 | ENST00000262965.12 | c.1940C>G | p.Ala647Gly | missense_variant | Exon 19 of 19 | 1 | NM_003200.5 | ENSP00000262965.5 | ||
TCF3 | ENST00000588136.7 | c.1931C>G | p.Ala644Gly | missense_variant | Exon 19 of 20 | 2 | NM_001136139.4 | ENSP00000468487.1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152110Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000639 AC: 16AN: 250328Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135566
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461436Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727012
GnomAD4 genome AF: 0.000204 AC: 31AN: 152110Hom.: 0 Cov.: 30 AF XY: 0.000202 AC XY: 15AN XY: 74308
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1940C>G (p.A647G) alteration is located in exon 19 (coding exon 18) of the TCF3 gene. This alteration results from a C to G substitution at nucleotide position 1940, causing the alanine (A) at amino acid position 647 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at