Genetic Variant ARMCX4:p.Glu502Lys (chrX-101490093-G-A) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_001256155.3(ARMCX4):c.1504G>A(p.Glu502Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0024 in 1,154,548 control chromosomes in the GnomAD database, including 3 homozygotes. There are 849 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0016 ( 0 hom., 46 hem., cov: 24)

Exomes 𝑓: 0.0025 ( 3 hom. 803 hem. )

Consequence

ARMCX4
NM_001256155.3 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:2

Conservation

PhyloP100: 1.66

Variant links:

Genes affected

ARMCX4 (HGNC:28615): (armadillo repeat containing X-linked 4) The product of this gene belongs to the armadillo repeat-containing family of proteins, which interact with other proteins in a variety of cellular processes. The function of this family member is currently unknown. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]

ARMCX4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.035895377).

BP6

Variant X-101490093-G-A is Benign according to our data. Variant chrX-101490093-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1206017.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-101490093-G-A is described in Lovd as [Likely_benign].

BS2

High Hemizygotes in GnomAd4 at 46 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARMCX4	NM_001256155.3 link	c.1504G>A	p.Glu502Lys	missense_variant	Exon 6 of 6	ENST00000423738.5	NP_001243084.2	Q5H9R4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARMCX4	ENST00000423738.5 link	c.1504G>A	p.Glu502Lys	missense_variant	Exon 6 of 6	5	NM_001256155.3	ENSP00000404304.3		Q5H9R4-1

Frequencies

GnomAD3 genomes

AF:

0.00155

AC:

174

AN:

112266

Hom.:

Cov.:

AF XY:

0.00134

AC XY:

AN XY:

34402

show subpopulations

Gnomad AFR

AF:

0.000485

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000937

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000163

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00271

Gnomad OTH

AF:

0.00267

GnomAD3 exomes

AF:

0.00162

AC:

158

AN:

97802

Hom.:

AF XY:

0.00148

AC XY:

AN XY:

36494

show subpopulations

Gnomad AFR exome

AF:

0.000390

Gnomad AMR exome

AF:

0.00135

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000214

Gnomad FIN exome

AF:

0.000246

Gnomad NFE exome

AF:

0.00316

Gnomad OTH exome

AF:

0.00163

GnomAD4 exome

AF:

0.00249

AC:

2593

AN:

1042224

Hom.:

Cov.:

AF XY:

0.00235

AC XY:

803

AN XY:

341264

show subpopulations

Gnomad4 AFR exome

AF:

0.000361

Gnomad4 AMR exome

AF:

0.00125

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000200

Gnomad4 FIN exome

AF:

0.000232

Gnomad4 NFE exome

AF:

0.00297

Gnomad4 OTH exome

AF:

0.00203

GnomAD4 genome

AF:

0.00156

AC:

175

AN:

112324

Hom.:

Cov.:

AF XY:

0.00133

AC XY:

AN XY:

34470

show subpopulations

Gnomad4 AFR

AF:

0.000484

Gnomad4 AMR

AF:

0.000936

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000163

Gnomad4 NFE

AF:

0.00273

Gnomad4 OTH

AF:

0.00264

Alfa

AF:

0.00175

Hom.:

Bravo

AF:

0.00155

TwinsUK

AF:

0.00351

AC:

ALSPAC

AF:

0.00277

AC:

ExAC

AF:

0.000415

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not provided

Benign:2

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.69

CADD

Benign

6.2

DANN

Benign

0.96

FATHMM_MKL

Benign

0.48

LIST_S2

Benign

0.52

M_CAP

Pathogenic

0.68

MetaRNN

Benign

0.036

MetaSVM

Benign

-0.95

PrimateAI

Benign

0.34

REVEL

Benign

0.097

Sift4G

Benign

0.073

Vest4

0.24

MVP

0.26

ClinPred

0.99

GERP RS

4.8

gMVP

0.31

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over