chr20-609715-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004609.4(TCF15):c.523G>A(p.Gly175Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000445 in 1,382,968 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004609.4 missense, splice_region
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: 0.000907 AC: 138AN: 152190Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000707 AC: 10AN: 14150Hom.: 0 AF XY: 0.000683 AC XY: 6AN XY: 8788
GnomAD4 exome AF: 0.000388 AC: 478AN: 1230662Hom.: 3 Cov.: 29 AF XY: 0.000369 AC XY: 222AN XY: 602174
GnomAD4 genome AF: 0.000906 AC: 138AN: 152306Hom.: 1 Cov.: 32 AF XY: 0.00136 AC XY: 101AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.523G>A (p.G175R) alteration is located in exon 1 (coding exon 1) of the TCF15 gene. This alteration results from a G to A substitution at nucleotide position 523, causing the glycine (G) at amino acid position 175 to be replaced by an arginine (R). 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