1-109066134-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_005645.4(TAF13):c.204+1G>T variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.000000688 in 1,452,680 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_005645.4 splice_donor, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAF13 | NM_005645.4 | c.204+1G>T | splice_donor_variant, intron_variant | ENST00000338366.6 | NP_005636.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAF13 | ENST00000338366.6 | c.204+1G>T | splice_donor_variant, intron_variant | 1 | NM_005645.4 | ENSP00000355051.4 | ||||
TAF13 | ENST00000692048.1 | c.204+1G>T | splice_donor_variant, intron_variant | ENSP00000508876.1 | ||||||
TAF13 | ENST00000461096.7 | c.90+1G>T | splice_donor_variant, intron_variant | 5 | ENSP00000433883.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.88e-7 AC: 1AN: 1452680Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 722816
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Intellectual disability, autosomal recessive 60 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Breda Genetics srl | Jan 14, 2021 | The variant c.204+1G>T in the TAF13 gene affects the donor splice site of intron 3 and is therefore highly likely to impact the splicing process by causing the retention of the following intron and the formation of an aberrant mRNA, which is unlikely to be exported and translated into protein. This variant has not been reported in dbSNP, gnomAD, 1000 Genomes Project or ClinVar. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.