chr16-30091481-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000553607.1(TBX6):c.-288A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 323,542 control chromosomes in the GnomAD database, including 17,041 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.26 ( 6425 hom., cov: 30)
Exomes 𝑓: 0.33 ( 10616 hom. )
Consequence
TBX6
ENST00000553607.1 5_prime_UTR
ENST00000553607.1 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.604
Genes affected
TBX6 (HGNC:11605): (T-box transcription factor 6) 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. Knockout studies in mice indicate that this gene is important for specification of paraxial mesoderm structures. [provided by RefSeq, Aug 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=-0.48).
BP6
?
Variant 16-30091481-T-C is Benign according to our data. Variant chr16-30091481-T-C is described in ClinVar as [Benign]. Clinvar id is 427808.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX6 | NM_004608.4 | c.-48-240A>G | intron_variant | ENST00000395224.7 | |||
TBX6 | XM_011545926.4 | c.-70A>G | 5_prime_UTR_variant | 1/9 | |||
TBX6 | XM_047434551.1 | c.-288A>G | 5_prime_UTR_variant | 1/8 | |||
TBX6 | XR_007064904.1 | n.54A>G | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX6 | ENST00000553607.1 | c.-288A>G | 5_prime_UTR_variant | 1/5 | 1 | ||||
TBX6 | ENST00000395224.7 | c.-48-240A>G | intron_variant | 1 | NM_004608.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.261 AC: 39385AN: 150622Hom.: 6424 Cov.: 30
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GnomAD4 exome AF: 0.331 AC: 57279AN: 172808Hom.: 10616 Cov.: 0 AF XY: 0.327 AC XY: 29253AN XY: 89520
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GnomAD4 genome ? AF: 0.261 AC: 39395AN: 150734Hom.: 6425 Cov.: 30 AF XY: 0.264 AC XY: 19436AN XY: 73526
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at