chrX-101488723-T-C

Variant names:

• chrX-101488723-T-C
• NM_001256155.3:c.134T>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001256155.3(ARMCX4):​c.134T>C​(p.Val45Ala) 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. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: ARMCX4 NM_001256155.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.84
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.22129092).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMCX4	NM_001256155.3	MANE Select	c.134T>C	p.Val45Ala	missense	Exon 6 of 6	NP_001243084.2	Q5H9R4-1
	ARMCX4	NR_028407.3		n.941T>C		non_coding_transcript_exon	Exon 9 of 16
	ARMCX4	NR_045861.2		n.645T>C		non_coding_transcript_exon	Exon 6 of 13

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMCX4	ENST00000423738.5	TSL:5 MANE Select	c.134T>C	p.Val45Ala	missense	Exon 6 of 6	ENSP00000404304.3	Q5H9R4-1
	ARMCX4	ENST00000354842.5	TSL:1	n.134T>C		non_coding_transcript_exon	Exon 6 of 13	ENSP00000423927.2	A0A8J9A6E2
	ARMCX4	ENST00000433011.6	TSL:1	n.134T>C		non_coding_transcript_exon	Exon 9 of 16	ENSP00000424452.2	A0A8J9A6E2

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.46
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	17
DANN	Uncertain	0.99
FATHMM_MKL	Benign	0.68	D
LIST_S2	Benign	0.38	T
M_CAP	Benign	0.060	D
MetaRNN	Benign	0.22	T
MetaSVM	Benign	-1.0	T
PhyloP100		1.8
PrimateAI	Benign	0.44	T
REVEL	Benign	0.15
Sift4G	Uncertain	0.0060	D
Vest4		0.31
MVP		0.35
ClinPred		0.74	D
GERP RS		4.9
gMVP		0.62
Mutation Taster		=94/6	polymorphism

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

hg19: chrX-100743710;