rs3833842
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_004608.4(TBX6):c.840-23_840-18del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000988 in 1,599,794 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00010 ( 0 hom. )
Consequence
TBX6
NM_004608.4 intron
NM_004608.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.06
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 16-30086868-GTGATGA-G is Benign according to our data. Variant chr16-30086868-GTGATGA-G is described in ClinVar as [Likely_benign]. Clinvar id is 1615180.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX6 | NM_004608.4 | c.840-23_840-18del | intron_variant | ENST00000395224.7 | |||
TBX6 | XM_011545926.4 | c.840-23_840-18del | intron_variant | ||||
TBX6 | XM_047434551.1 | c.840-23_840-18del | intron_variant | ||||
TBX6 | XR_007064904.1 | n.1038_1043del | non_coding_transcript_exon_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX6 | ENST00000395224.7 | c.840-23_840-18del | intron_variant | 1 | NM_004608.4 | P1 | |||
TBX6 | ENST00000279386.6 | c.840-23_840-18del | intron_variant | 1 | P1 | ||||
TBX6 | ENST00000567664.5 | c.*48-179_*48-174del | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151724Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.000104 AC: 151AN: 1447952Hom.: 0 AF XY: 0.000110 AC XY: 79AN XY: 719516
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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 | Oct 13, 2023 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at