chr17-61456587-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001321120.2(TBX4):c.97G>T(p.Ala33Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000032 in 1,530,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001321120.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX4 | NM_001321120.2 | c.97G>T | p.Ala33Ser | missense_variant | 2/9 | ENST00000644296.1 | |
LOC124904042 | XR_007065872.1 | n.2116C>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX4 | ENST00000644296.1 | c.97G>T | p.Ala33Ser | missense_variant | 2/9 | NM_001321120.2 | A1 | ||
TBX4 | ENST00000240335.1 | c.97G>T | p.Ala33Ser | missense_variant | 1/8 | 1 | P4 | ||
TBX4 | ENST00000642491.1 | c.97G>T | p.Ala33Ser | missense_variant | 1/8 | A1 | |||
TBX4 | ENST00000589003.5 | c.-125-37G>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152004Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000157 AC: 2AN: 127590Hom.: 0 AF XY: 0.0000144 AC XY: 1AN XY: 69574
GnomAD4 exome AF: 0.0000319 AC: 44AN: 1378880Hom.: 0 Cov.: 32 AF XY: 0.0000309 AC XY: 21AN XY: 679832
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152004Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74234
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.97G>T (p.A33S) alteration is located in exon 1 (coding exon 1) of the TBX4 gene. This alteration results from a G to T substitution at nucleotide position 97, causing the alanine (A) at amino acid position 33 to be replaced by a serine (S). 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