12-51110869-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_005653.5(TFCP2):c.564+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000226 in 1,595,140 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (no stars).
Frequency
Consequence
NM_005653.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TFCP2 | NM_005653.5 | c.564+8G>A | splice_region_variant, intron_variant | Intron 5 of 14 | ENST00000257915.10 | NP_005644.2 | ||
TFCP2 | NM_001173452.2 | c.564+8G>A | splice_region_variant, intron_variant | Intron 5 of 14 | NP_001166923.1 | |||
TFCP2 | NM_001173453.2 | c.564+8G>A | splice_region_variant, intron_variant | Intron 5 of 13 | NP_001166924.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 250982Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135682
GnomAD4 exome AF: 0.000237 AC: 342AN: 1443002Hom.: 0 Cov.: 28 AF XY: 0.000243 AC XY: 175AN XY: 719042
GnomAD4 genome AF: 0.000118 AC: 18AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74306
ClinVar
Submissions by phenotype
TFCP2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at