rs4656579
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005149.3(TBX19):c.728-45G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 1,592,222 control chromosomes in the GnomAD database, including 357,890 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.61 ( 28832 hom., cov: 32)
Exomes 𝑓: 0.67 ( 329058 hom. )
Consequence
TBX19
NM_005149.3 intron
NM_005149.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.642
Genes affected
TBX19 (HGNC:11596): (T-box transcription factor 19) This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. Mutations in this gene were found in patients with isolated deficiency of pituitary POMC-derived ACTH, suggesting an essential role for this gene in differentiation of the pituitary POMC lineage. ACTH deficiency is characterized by adrenal insufficiency symptoms such as weight loss, lack of appetite (anorexia), weakness, nausea, vomiting, and low blood pressure. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 1-168304963-G-A is Benign according to our data. Variant chr1-168304963-G-A is described in ClinVar as [Benign]. Clinvar id is 1334932.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX19 | NM_005149.3 | c.728-45G>A | intron_variant | ENST00000367821.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX19 | ENST00000367821.8 | c.728-45G>A | intron_variant | 1 | NM_005149.3 | P1 | |||
TBX19 | ENST00000431969.5 | c.525-3779G>A | intron_variant | 5 | |||||
TBX19 | ENST00000441464.1 | c.225-45G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.605 AC: 91957AN: 151944Hom.: 28810 Cov.: 32
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GnomAD3 exomes AF: 0.603 AC: 148695AN: 246620Hom.: 46733 AF XY: 0.602 AC XY: 80637AN XY: 133844
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GnomAD4 exome AF: 0.669 AC: 963900AN: 1440160Hom.: 329058 Cov.: 27 AF XY: 0.664 AC XY: 476576AN XY: 717862
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GnomAD4 genome ? AF: 0.605 AC: 92022AN: 152062Hom.: 28832 Cov.: 32 AF XY: 0.594 AC XY: 44118AN XY: 74332
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital isolated adrenocorticotropic hormone deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at