rs17331728

Positions:

• chrX-102699540-G-C

Variant summary

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

The NM_001199818.1(ARMCX5-GPRASP2):​c.-479-14242G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 111,391 control chromosomes in the GnomAD database, including 583 homozygotes. There are 3,240 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 0.10 (583 hom., 3240 hem., cov: 23)
• Consequence: ARMCX5-GPRASP2 NM_001199818.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

Genes affected

ARMCX5-GPRASP2 (HGNC:42000): (ARMCX5-GPRASP2 readthrough) This locus represents naturally occurring readthrough transcription among the adjacent armadillo repeat containing, X-linked 5 (ARMCX5), G protein-coupled receptor associated sorting proteins 1 and 2 (GPRASP1 and GPRASP2), basic helix-loop-helix family member b9 (BHLHB9), and long intergenic non-protein coding RNA 630 (LINC00630) genes on chromosome X. Transcripts may make use of multiple alternative promoters and polyadenylation signals in this region. Readthrough transcripts may produce proteins identical to the proteins encoded by GPRASP2 or BHLHB9. [provided by RefSeq, Apr 2017]

ARMCX5-GPRASP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMCX5-GPRASP2	NM_001199818.1	c.-479-14242G>C		intron_variant			NP_001186747.1
ARMCX5-GPRASP2	NM_001350268.2	c.-965-14242G>C		intron_variant			NP_001337197.1
ARMCX5-GPRASP2	NR_146584.3	n.650-14242G>C		intron_variant
ARMCX5-GPRASP2	NR_146585.2	n.151-14242G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARMCX5-GPRASP2	ENST00000486740.6	n.409-14242G>C		intron_variant		3
ARMCX5-GPRASP2	ENST00000602366.5	n.495-14242G>C		intron_variant		4
ARMCX5-GPRASP2	ENST00000602463.5	n.370-14242G>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.102 AC: 11304 AN: 111349 Hom.: 583 Cov.: 23 AF XY: 0.0964 AC XY: 3239 AN XY: 33585

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.0952

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.000553

Gnomad SAS AF: 0.0309

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.101 AC: 11300 AN: 111391 Hom.: 583 Cov.: 23 AF XY: 0.0963 AC XY: 3240 AN XY: 33637

Gnomad4 AFR AF: 0.0221

Gnomad4 AMR AF: 0.0893

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.000554

Gnomad4 SAS AF: 0.0317

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.116

Alfa AF: 0.124 Hom.: 817

Bravo AF: 0.0946

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17331728; hg19: chrX-101954468;