chr11-67632328-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_005995.5(TBX10):c.858C>T(p.Asp286=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,613,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
TBX10
NM_005995.5 synonymous
NM_005995.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.327
Genes affected
TBX10 (HGNC:11593): (T-box transcription factor 10) This gene encodes a member of the T-box family of transcription factors. These transcription factors share a DNA-binding domain called the T-box, and play a role in several developmental processes including early embryonic cell fate and organogenesis. The encoded protein is a member of the T-box 1 subfamily. Mutations in this gene are thought to be a cause of isolated cleft lip with or without cleft palate. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 11-67632328-G-A is Benign according to our data. Variant chr11-67632328-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3040657.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.327 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX10 | NM_005995.5 | c.858C>T | p.Asp286= | synonymous_variant | 7/8 | ENST00000335385.4 | |
TBX10 | XM_047426879.1 | c.1731C>T | p.Asp577= | synonymous_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX10 | ENST00000335385.4 | c.858C>T | p.Asp286= | synonymous_variant | 7/8 | 1 | NM_005995.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152236Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000455 AC: 114AN: 250286Hom.: 1 AF XY: 0.000398 AC XY: 54AN XY: 135586
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GnomAD4 exome AF: 0.000140 AC: 204AN: 1461012Hom.: 0 Cov.: 34 AF XY: 0.000127 AC XY: 92AN XY: 726816
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GnomAD4 genome AF: 0.000217 AC: 33AN: 152354Hom.: 0 Cov.: 34 AF XY: 0.000295 AC XY: 22AN XY: 74498
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TBX10-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 20, 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at