X-101491271-T-C

Variant names:

• chrX-101491271-T-C
• rs1603211585
• NM_001256155.3:c.2682T>C

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_001256155.3(ARMCX4):​c.2682T>C​(p.Val894Val) variant causes a synonymous 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. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 27)
• Consequence: ARMCX4 NM_001256155.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.598
• 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: Likely_benign. The variant received -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant X-101491271-T-C is Benign according to our data. Variant chrX-101491271-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 3234258.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.598 with no splicing effect.

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.2682T>C	p.Val894Val	synonymous	Exon 6 of 6	NP_001243084.2	Q5H9R4-1
	ARMCX4	NR_028407.3		n.1533+1956T>C		intron	N/A
	ARMCX4	NR_045861.2		n.1237+1956T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMCX4	ENST00000423738.5	TSL:5 MANE Select	c.2682T>C	p.Val894Val	synonymous	Exon 6 of 6	ENSP00000404304.3	Q5H9R4-1
	ARMCX4	ENST00000354842.5	TSL:1	n.726+1956T>C		intron	N/A	ENSP00000423927.2	A0A8J9A6E2
	ARMCX4	ENST00000433011.6	TSL:1	n.726+1956T>C		intron	N/A	ENSP00000424452.2	A0A8J9A6E2

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome Cov.: 38

GnomAD4 genome Cov.: 27

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions as Germline

Significance: Likely benign

Revision: criteria provided, single submitter

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		-0.60

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: rs1603211585; hg19: chrX-100746258; COSMIC: COSV61448840;