rs4612544

Positions:

• chrX-71106804-A-G

Variant summary

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

The X-71106804-A-G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 712,380 control chromosomes in the GnomAD database, including 4,433 homozygotes. There are 24,361 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 0.15 (1071 hom., 4573 hem., cov: 22)
  • Exomes 𝑓: 0.12 (3362 hom. 19788 hem.)
• Consequence: CXorf65 ENST00000438526.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.682

Genes affected

CXorf65 (HGNC:33713): (chromosome X open reading frame 65)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CXorf65	ENST00000438526.2			upstream_gene_variant		1		ENSP00000411354

Frequencies

GnomAD3 genomes AF: 0.148 AC: 16353 AN: 110765 Hom.: 1067 Cov.: 22 AF XY: 0.138 AC XY: 4554 AN XY: 33017

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.133

GnomAD4 exome AF: 0.124 AC: 74300 AN: 601561 Hom.: 3362 Cov.: 9 AF XY: 0.151 AC XY: 19788 AN XY: 131425

Gnomad4 AFR exome AF: 0.263

Gnomad4 AMR exome AF: 0.104

Gnomad4 ASJ exome AF: 0.0719

Gnomad4 EAS exome AF: 0.111

Gnomad4 SAS exome AF: 0.206

Gnomad4 FIN exome AF: 0.115

Gnomad4 NFE exome AF: 0.117

Gnomad4 OTH exome AF: 0.132

GnomAD4 genome AF: 0.148 AC: 16375 AN: 110819 Hom.: 1071 Cov.: 22 AF XY: 0.138 AC XY: 4573 AN XY: 33081

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0727

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.143

Alfa AF: 0.136 Hom.: 877

Bravo AF: 0.154

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.6
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4612544; hg19: chrX-70326654; COSMIC: COSV52150492;