X-120159308-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000371388.5(RHOXF2):c.373G>A(p.Val125Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000787 in 1,207,025 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 32 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000371388.5 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 |
---|---|---|---|---|---|---|---|---|
RHOXF2 | NM_032498.3 | c.373G>A | p.Val125Ile | missense_variant | 2/4 | ENST00000371388.5 | NP_115887.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RHOXF2 | ENST00000371388.5 | c.373G>A | p.Val125Ile | missense_variant | 2/4 | 1 | NM_032498.3 | ENSP00000360441.3 |
Frequencies
GnomAD3 genomes AF: 0.0000711 AC: 8AN: 112501Hom.: 0 Cov.: 19 AF XY: 0.0000576 AC XY: 2AN XY: 34713
GnomAD3 exomes AF: 0.000115 AC: 17AN: 148119Hom.: 0 AF XY: 0.000237 AC XY: 11AN XY: 46457
GnomAD4 exome AF: 0.0000795 AC: 87AN: 1094479Hom.: 0 Cov.: 31 AF XY: 0.0000832 AC XY: 30AN XY: 360375
GnomAD4 genome AF: 0.0000711 AC: 8AN: 112546Hom.: 0 Cov.: 19 AF XY: 0.0000575 AC XY: 2AN XY: 34768
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 14, 2024 | The c.373G>A (p.V125I) alteration is located in exon 2 (coding exon 2) of the RHOXF2 gene. This alteration results from a G to A substitution at nucleotide position 373, causing the valine (V) at amino acid position 125 to be replaced by an isoleucine (I). 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