chrX-102602314-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001168478.2(ARMCX5):​c.173C>A​(p.Ala58Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A58V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 23)

Consequence

ARMCX5
NM_001168478.2 missense

Scores

2
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.683
Variant links:
Genes affected
ARMCX5 (HGNC:25772): (armadillo repeat containing X-linked 5)
ARMCX5-GPRASP2 (HGNC:42000): (ARMCX5-GPRASP2 readthrough) This locus represents naturally occurring readthrough transcription among the adjacent armadillo repeat containing, X-linked 5 (ARMCX5), G protein-coupled receptor associated sorting proteins 1 and 2 (GPRASP1 and GPRASP2), basic helix-loop-helix family member b9 (BHLHB9), and long intergenic non-protein coding RNA 630 (LINC00630) genes on chromosome X. Transcripts may make use of multiple alternative promoters and polyadenylation signals in this region. Readthrough transcripts may produce proteins identical to the proteins encoded by GPRASP2 or BHLHB9. [provided by RefSeq, Apr 2017]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0801577).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARMCX5NM_001168478.2 linkc.173C>A p.Ala58Glu missense_variant Exon 4 of 4 ENST00000473968.7 NP_001161950.1 Q6P1M9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ARMCX5ENST00000473968.7 linkc.173C>A p.Ala58Glu missense_variant Exon 4 of 4 2 NM_001168478.2 ENSP00000473737.2 Q6P1M9A0A0G2JLJ9

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.32
T
BayesDel_noAF
Benign
-0.69
CADD
Benign
6.5
DANN
Benign
0.85
DEOGEN2
Benign
0.032
T;T;.;.;T
FATHMM_MKL
Benign
0.21
N
LIST_S2
Benign
0.37
.;.;T;T;T
M_CAP
Benign
0.0034
T
MetaRNN
Benign
0.080
T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.5
L;L;.;.;L
PrimateAI
Benign
0.26
T
PROVEAN
Benign
-1.4
N;.;.;.;N
REVEL
Benign
0.043
Sift
Uncertain
0.0040
D;.;.;.;D
Sift4G
Uncertain
0.0090
D;D;D;D;D
Polyphen
0.84
P;P;.;.;P
Vest4
0.31
MutPred
0.20
Loss of MoRF binding (P = 0.0324);Loss of MoRF binding (P = 0.0324);Loss of MoRF binding (P = 0.0324);Loss of MoRF binding (P = 0.0324);Loss of MoRF binding (P = 0.0324);
MVP
0.082
MPC
0.17
ClinPred
0.20
T
GERP RS
1.9
Varity_R
0.16
gMVP
0.11

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-101857242; API