X-101657225-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_177949.4(ARMCX2):c.364G>T(p.Gly122Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,200,137 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. 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_177949.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARMCX2 | NM_177949.4 | c.364G>T | p.Gly122Trp | missense_variant | Exon 6 of 6 | ENST00000356824.9 | NP_808818.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000124 AC: 14AN: 113260Hom.: 0 Cov.: 24 AF XY: 0.000113 AC XY: 4AN XY: 35404
GnomAD3 exomes AF: 0.00000577 AC: 1AN: 173249Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 59149
GnomAD4 exome AF: 0.00000276 AC: 3AN: 1086877Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 354897
GnomAD4 genome AF: 0.000124 AC: 14AN: 113260Hom.: 0 Cov.: 24 AF XY: 0.000113 AC XY: 4AN XY: 35404
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.364G>T (p.G122W) alteration is located in exon 6 (coding exon 1) of the ARMCX2 gene. This alteration results from a G to T substitution at nucleotide position 364, causing the glycine (G) at amino acid position 122 to be replaced by a tryptophan (W). 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