5-134138075-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003202.5(TCF7):c.458C>A(p.Pro153His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000804 in 1,603,640 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 Uncertain significance (★).
Frequency
Consequence
NM_003202.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152010Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000873 AC: 21AN: 240518Hom.: 0 AF XY: 0.0000615 AC XY: 8AN XY: 130132
GnomAD4 exome AF: 0.0000530 AC: 77AN: 1451512Hom.: 0 Cov.: 30 AF XY: 0.0000499 AC XY: 36AN XY: 722028
GnomAD4 genome AF: 0.000342 AC: 52AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.458C>A (p.P153H) alteration is located in exon 4 (coding exon 4) of the TCF7 gene. This alteration results from a C to A substitution at nucleotide position 458, causing the proline (P) at amino acid position 153 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at