rs5951332

Variant names:

• chrX-101488839-A-G
• rs5951332
• NM_001256155.3:c.250A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001256155.3(ARMCX4):​c.250A>G​(p.Arg84Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.69 (19074 hom., 22145 hem., cov: 23)
  • Exomes 𝑓: 0.69 (171939 hom. 235199 hem.)
  • Failed GnomAD Quality Control
• Consequence: ARMCX4 NM_001256155.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395
• Publications: 19 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=3.290057E-5).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256155.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMCX4	NM_001256155.3	MANE Select	c.250A>G	p.Arg84Gly	missense	Exon 6 of 6	NP_001243084.2
	ARMCX4	NR_028407.3		n.1057A>G		non_coding_transcript_exon	Exon 9 of 16
	ARMCX4	NR_045861.2		n.761A>G		non_coding_transcript_exon	Exon 6 of 13

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMCX4	ENST00000423738.5	TSL:5 MANE Select	c.250A>G	p.Arg84Gly	missense	Exon 6 of 6	ENSP00000404304.3
	ARMCX4	ENST00000354842.5	TSL:1	n.250A>G		non_coding_transcript_exon	Exon 6 of 13	ENSP00000423927.2
	ARMCX4	ENST00000433011.6	TSL:1	n.250A>G		non_coding_transcript_exon	Exon 9 of 16	ENSP00000424452.2

Frequencies

GnomAD3 genomes AF: 0.692 AC: 76393 AN: 110472 Hom.: 19075 Cov.: 23

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.701

GnomAD2 exomes AF: 0.638 AC: 65472 AN: 102571 AF XY: 0.635

Gnomad AFR exome AF: 0.730

Gnomad AMR exome AF: 0.531

Gnomad ASJ exome AF: 0.724

Gnomad EAS exome AF: 0.458

Gnomad FIN exome AF: 0.684

Gnomad NFE exome AF: 0.724

Gnomad OTH exome AF: 0.667

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.694 AC: 723581 AN: 1042326 Hom.: 171939 Cov.: 49 AF XY: 0.689 AC XY: 235199 AN XY: 341218

African (AFR) AF: 0.731 AC: 18218 AN: 24911

American (AMR) AF: 0.541 AC: 15094 AN: 27911

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 13568 AN: 18643

East Asian (EAS) AF: 0.418 AC: 11341 AN: 27133

South Asian (SAS) AF: 0.544 AC: 27119 AN: 49882

European-Finnish (FIN) AF: 0.672 AC: 17425 AN: 25927

Middle Eastern (MID) AF: 0.690 AC: 2822 AN: 4088

European-Non Finnish (NFE) AF: 0.717 AC: 587575 AN: 819462

Other (OTH) AF: 0.686 AC: 30419 AN: 44369

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.691 AC: 76421 AN: 110530 Hom.: 19074 Cov.: 23 AF XY: 0.676 AC XY: 22145 AN XY: 32766

African (AFR) AF: 0.726 AC: 22049 AN: 30388

American (AMR) AF: 0.590 AC: 6117 AN: 10370

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 1904 AN: 2640

East Asian (EAS) AF: 0.446 AC: 1540 AN: 3451

South Asian (SAS) AF: 0.507 AC: 1331 AN: 2627

European-Finnish (FIN) AF: 0.663 AC: 3870 AN: 5834

Middle Eastern (MID) AF: 0.631 AC: 135 AN: 214

European-Non Finnish (NFE) AF: 0.717 AC: 37879 AN: 52839

Other (OTH) AF: 0.699 AC: 1043 AN: 1493

Alfa AF: 0.707 Hom.: 30078

Bravo AF: 0.690

TwinsUK AF: 0.710 AC: 2633

ALSPAC AF: 0.715 AC: 2067

ExAC AF: 0.611 AC: 11232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.065
BayesDel_addAF	Benign	-0.87	T
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.80
FATHMM_MKL	Benign	0.0071	N
LIST_S2	Benign	0.19	T
MetaRNN	Benign	0.000033	T
MetaSVM	Benign	-0.94	T
PhyloP100		0.40
PrimateAI	Benign	0.23	T
REVEL	Benign	0.011
Sift4G	Benign	0.59	T
Vest4		0.032
ClinPred		0.0084	T
GERP RS		-1.0
gMVP		0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5951332; hg19: chrX-100743826;