NM_003200.5:c.1948C>A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_003200.5(TCF3):c.1948C>A(p.Pro650Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000187 in 1,613,622 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 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.1948C>A | p.Pro650Thr | missense_variant | Exon 19 of 19 | 1 | NM_003200.5 | ENSP00000262965.5 | ||
TCF3 | ENST00000588136.7 | c.1939C>A | p.Pro647Thr | missense_variant | Exon 19 of 20 | 2 | NM_001136139.4 | ENSP00000468487.1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152120Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000200 AC: 50AN: 250136Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135464
GnomAD4 exome AF: 0.000193 AC: 282AN: 1461384Hom.: 1 Cov.: 31 AF XY: 0.000197 AC XY: 143AN XY: 726982
GnomAD4 genome AF: 0.000125 AC: 19AN: 152238Hom.: 0 Cov.: 31 AF XY: 0.000148 AC XY: 11AN XY: 74438
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
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Inborn genetic diseases Uncertain:1
The c.1948C>A (p.P650T) alteration is located in exon 19 (coding exon 18) of the TCF3 gene. This alteration results from a C to A substitution at nucleotide position 1948, causing the proline (P) at amino acid position 650 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Agammaglobulinemia 8, autosomal dominant;C5676958:Agammaglobulinemia 8b, autosomal recessive Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at