17-61456513-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BS2_Supporting
The NM_001321120.2(TBX4):c.23C>T(p.Ser8Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000434 in 1,568,234 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S8S) has been classified as Benign.
Frequency
Consequence
NM_001321120.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBX4 | ENST00000644296.1 | c.23C>T | p.Ser8Phe | missense_variant | Exon 2 of 9 | NM_001321120.2 | ENSP00000495986.1 | |||
TBX4 | ENST00000240335.1 | c.23C>T | p.Ser8Phe | missense_variant | Exon 1 of 8 | 1 | ENSP00000240335.1 | |||
TBX4 | ENST00000642491.1 | c.23C>T | p.Ser8Phe | missense_variant | Exon 1 of 8 | ENSP00000495714.1 | ||||
TBX4 | ENST00000589003.5 | c.-125-111C>T | intron_variant | Intron 1 of 5 | 3 | ENSP00000467588.1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152134Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000417 AC: 59AN: 1416100Hom.: 0 Cov.: 32 AF XY: 0.0000343 AC XY: 24AN XY: 700210
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152134Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74304
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.23C>T (p.S8F) alteration is located in exon 1 (coding exon 1) of the TBX4 gene. This alteration results from a C to T substitution at nucleotide position 23, causing the serine (S) at amino acid position 8 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at