chrX-120076998-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001099685.3(RHOXF2B):c.370G>A(p.Ala124Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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
NM_001099685.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 3AN: 72848Hom.: 0 Cov.: 12 AF XY: 0.0000665 AC XY: 1AN XY: 15028 FAILED QC
GnomAD3 exomes AF: 0.0000107 AC: 1AN: 93421Hom.: 0 AF XY: 0.0000401 AC XY: 1AN XY: 24949
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000949 AC: 9AN: 948553Hom.: 1 Cov.: 28 AF XY: 0.0000148 AC XY: 4AN XY: 270555
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000412 AC: 3AN: 72848Hom.: 0 Cov.: 12 AF XY: 0.0000665 AC XY: 1AN XY: 15028
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.370G>A (p.A124T) alteration is located in exon 2 (coding exon 2) of the RHOXF2B gene. This alteration results from a G to A substitution at nucleotide position 370, causing the alanine (A) at amino acid position 124 to be replaced by a threonine (T). 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