11-67631708-T-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005995.5(TBX10):āc.1055A>Cā(p.Asn352Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000217 in 1,609,462 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_005995.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX10 | NM_005995.5 | c.1055A>C | p.Asn352Thr | missense_variant | 8/8 | ENST00000335385.4 | |
TBX10 | XM_047426879.1 | c.1928A>C | p.Asn643Thr | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX10 | ENST00000335385.4 | c.1055A>C | p.Asn352Thr | missense_variant | 8/8 | 1 | NM_005995.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00125 AC: 299AN: 238608Hom.: 3 AF XY: 0.000788 AC XY: 102AN XY: 129422
GnomAD4 exome AF: 0.000222 AC: 323AN: 1457332Hom.: 3 Cov.: 32 AF XY: 0.000161 AC XY: 117AN XY: 724504
GnomAD4 genome AF: 0.000171 AC: 26AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74402
ClinVar
Submissions by phenotype
TBX10-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 03, 2020 | This variant is classified as 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