rs11092309

Positions:

• chrX-101482738-G-A
• chrX-101482738-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433011.6(ARMCX4):​c.-472-3285G>A variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 109,135 control chromosomes in the GnomAD database, including 10,817 homozygotes. There are 15,426 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (10817 hom., 15426 hem., cov: 21)
• Consequence: ARMCX4 ENST00000433011.6 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMCX4	NR_028407.3	n.336-3285G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMCX4	ENST00000433011.6	c.-472-3285G>A		intron_variant, NMD_transcript_variant		1		ENSP00000424452

Frequencies

GnomAD3 genomes AF: 0.497 AC: 54251 AN: 109092 Hom.: 10808 Cov.: 21 AF XY: 0.490 AC XY: 15389 AN XY: 31404

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.466

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.460

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.498 AC: 54298 AN: 109135 Hom.: 10817 Cov.: 21 AF XY: 0.490 AC XY: 15426 AN XY: 31457

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.465

Alfa AF: 0.448 Hom.: 4599

Bravo AF: 0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11092309; hg19: chrX-100737725;