rs17331728

chrX-102699540-G-C

Variant summary

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

The NR_146584.3(ARMCX5-GPRASP2):n.650-14242G>C variant causes a intron, non coding transcript 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 NR_146584.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

Genes affected

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	UniProt
ARMCX5-GPRASP2	NR_146584.3	n.650-14242G>C		intron_variant, non_coding_transcript_variant
ARMCX5-GPRASP2	NM_001199818.1	c.-479-14242G>C		intron_variant
ARMCX5-GPRASP2	NM_001350268.2	c.-965-14242G>C		intron_variant
ARMCX5-GPRASP2	NR_146585.2	n.151-14242G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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;