1-118884858-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001330677.2(TBX15):c.1683G>A(p.Gly561=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,614,042 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 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
TBX15
NM_001330677.2 synonymous
NM_001330677.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.198
Genes affected
TBX15 (HGNC:11594): (T-box transcription factor 15) This gene belongs to the T-box family of genes, which encode a phylogenetically conserved family of transcription factors that regulate a variety of developmental processes. All these genes contain a common T-box DNA-binding domain. Mutations in this gene are associated with Cousin syndrome.[provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
Variant 1-118884858-C-T is Benign according to our data. Variant chr1-118884858-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2171772.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.198 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX15 | NM_001330677.2 | c.1683G>A | p.Gly561= | synonymous_variant | 8/8 | ENST00000369429.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX15 | ENST00000369429.5 | c.1683G>A | p.Gly561= | synonymous_variant | 8/8 | 5 | NM_001330677.2 | P1 | |
TBX15 | ENST00000207157.7 | c.1365G>A | p.Gly455= | synonymous_variant | 8/8 | 1 | |||
TBX15 | ENST00000449873.5 | c.867G>A | p.Gly289= | synonymous_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250862Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135544
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461864Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727234
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 02, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
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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