chr11-67631901-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005995.5(TBX10):c.869-7C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000831 in 1,563,616 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 (★).
Frequency
Consequence
NM_005995.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX10 | NM_005995.5 | c.869-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000335385.4 | |||
TBX10 | XM_047426879.1 | c.1742-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX10 | ENST00000335385.4 | c.869-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005995.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000233 AC: 39AN: 167554Hom.: 0 AF XY: 0.000214 AC XY: 19AN XY: 88664
GnomAD4 exome AF: 0.0000801 AC: 113AN: 1411346Hom.: 0 Cov.: 32 AF XY: 0.0000789 AC XY: 55AN XY: 696706
GnomAD4 genome AF: 0.000112 AC: 17AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74436
ClinVar
Submissions by phenotype
TBX10-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 25, 2019 | 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