chr7-151148980-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001098834.3(GBX1):c.701C>T(p.Pro234Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001098834.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GBX1 | NM_001098834.3 | c.701C>T | p.Pro234Leu | missense_variant | 2/2 | ENST00000297537.5 | NP_001092304.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GBX1 | ENST00000297537.5 | c.701C>T | p.Pro234Leu | missense_variant | 2/2 | 1 | NM_001098834.3 | ENSP00000297537 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152036Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000561 AC: 14AN: 249466Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135358
GnomAD4 exome AF: 0.000105 AC: 154AN: 1461812Hom.: 0 Cov.: 32 AF XY: 0.000117 AC XY: 85AN XY: 727220
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2022 | The c.701C>T (p.P234L) alteration is located in exon 2 (coding exon 2) of the GBX1 gene. This alteration results from a C to T substitution at nucleotide position 701, causing the proline (P) at amino acid position 234 to be replaced by a leucine (L). 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