X-104250463-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_153448.4(ESX1):c.986G>A(p.Arg329His) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153448.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000455 AC: 3AN: 65886Hom.: 0 Cov.: 15 AF XY: 0.00 AC XY: 0AN XY: 15636
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000617 AC: 5AN: 810824Hom.: 0 Cov.: 31 AF XY: 0.0000123 AC XY: 3AN XY: 244152
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000455 AC: 3AN: 65886Hom.: 0 Cov.: 15 AF XY: 0.00 AC XY: 0AN XY: 15636
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.986G>A (p.R329H) alteration is located in exon 4 (coding exon 4) of the ESX1 gene. This alteration results from a G to A substitution at nucleotide position 986, causing the arginine (R) at amino acid position 329 to be replaced by a histidine (H). 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