20-604625-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004609.4(TCF15):c.566G>T(p.Arg189Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000252 in 1,554,280 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_004609.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000815 AC: 13AN: 159480Hom.: 0 AF XY: 0.0000711 AC XY: 6AN XY: 84434
GnomAD4 exome AF: 0.000262 AC: 367AN: 1402092Hom.: 0 Cov.: 31 AF XY: 0.000264 AC XY: 183AN XY: 691912
GnomAD4 genome AF: 0.000158 AC: 24AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.566G>T (p.R189M) alteration is located in exon 2 (coding exon 2) of the TCF15 gene. This alteration results from a G to T substitution at nucleotide position 566, causing the arginine (R) at amino acid position 189 to be replaced by a methionine (M). 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