NM_001256155.3:c.3312C>T

Variant names:

• chrX-101491901-C-T
• rs986906315
• NM_001256155.3:c.3312C>T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001256155.3(ARMCX4):​c.3312C>T​(p.Asp1104Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000048 in 1,041,843 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 25)
  • Exomes 𝑓: 0.0000048 (0 hom. 2 hem.)
• Consequence: ARMCX4 NM_001256155.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.658
• 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: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BP6: Variant X-101491901-C-T is Benign according to our data. Variant chrX-101491901-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2661063.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.658 with no splicing effect.
• BS2: High Hemizygotes in GnomAdExome4 at 2 gene

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.3312C>T	p.Asp1104Asp	synonymous	Exon 6 of 6	NP_001243084.2	Q5H9R4-1
	ARMCX4	NR_028407.3		n.1533+2586C>T		intron	N/A
	ARMCX4	NR_045861.2		n.1237+2586C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARMCX4	ENST00000423738.5	TSL:5 MANE Select	c.3312C>T	p.Asp1104Asp	synonymous	Exon 6 of 6	ENSP00000404304.3	Q5H9R4-1
	ARMCX4	ENST00000354842.5	TSL:1	n.726+2586C>T		intron	N/A	ENSP00000423927.2	A0A8J9A6E2
	ARMCX4	ENST00000433011.6	TSL:1	n.726+2586C>T		intron	N/A	ENSP00000424452.2	A0A8J9A6E2

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome AF: 0.00000480 AC: 5 AN: 1041843 Hom.: 0 Cov.: 37 AF XY: 0.00000587 AC XY: 2 AN XY: 340875

African (AFR) AF: 0.00 AC: 0 AN: 24909

American (AMR) AF: 0.00 AC: 0 AN: 27892

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18611

East Asian (EAS) AF: 0.00 AC: 0 AN: 27133

South Asian (SAS) AF: 0.00 AC: 0 AN: 49810

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 25898

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4088

European-Non Finnish (NFE) AF: 0.00000610 AC: 5 AN: 819218

Other (OTH) AF: 0.00 AC: 0 AN: 44284

GnomAD4 genome Cov.: 25

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

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	-0.50
CADD	Benign	2.6
DANN	Benign	0.53
PhyloP100		-0.66

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: rs986906315; hg19: chrX-100746888;