chr11-67634189-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005995.5(TBX10):c.549C>T(p.His183=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000499 in 1,612,606 control chromosomes in the GnomAD database, including 3 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 Likely benign (★).
Frequency
Consequence
NM_005995.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX10 | NM_005995.5 | c.549C>T | p.His183= | splice_region_variant, synonymous_variant | 4/8 | ENST00000335385.4 | |
TBX10 | XM_047426879.1 | c.1422C>T | p.His474= | splice_region_variant, synonymous_variant | 7/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX10 | ENST00000335385.4 | c.549C>T | p.His183= | splice_region_variant, synonymous_variant | 4/8 | 1 | NM_005995.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000368 AC: 56AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000811 AC: 203AN: 250370Hom.: 1 AF XY: 0.000738 AC XY: 100AN XY: 135578
GnomAD4 exome AF: 0.000512 AC: 748AN: 1460286Hom.: 3 Cov.: 34 AF XY: 0.000480 AC XY: 349AN XY: 726524
GnomAD4 genome AF: 0.000368 AC: 56AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.000430 AC XY: 32AN XY: 74494
ClinVar
Submissions by phenotype
TBX10-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 23, 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