rs1927232

chrX-68163049-C-T

Variant summary

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

The NM_002547.3(OPHN1):c.1276+29870G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 109,871 control chromosomes in the GnomAD database, including 5,544 homozygotes. There are 10,723 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 0.35 (5544 hom., 10723 hem., cov: 22)
• Consequence: OPHN1 NM_002547.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

OPHN1 (HGNC:8148): (oligophrenin 1) This gene encodes a Rho-GTPase-activating protein that promotes GTP hydrolysis of Rho subfamily members. Rho proteins are important mediators of intracellular signal transduction, which affects cell migration and cell morphogenesis. Mutations in this gene are responsible for OPHN1-related X-linked cognitive disability with cerebellar hypoplasia and distinctive facial dysmorhphism. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OPHN1	NM_002547.3	c.1276+29870G>A		intron_variant		ENST00000355520.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OPHN1	ENST00000355520.6	c.1276+29870G>A		intron_variant		1	NM_002547.3	P1

Frequencies

GnomAD3 genomes AF: 0.351 AC: 38516 AN: 109830 Hom.: 5535 Cov.: 22 AF XY: 0.331 AC XY: 10701 AN XY: 32302

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.351 AC: 38559 AN: 109871 Hom.: 5544 Cov.: 22 AF XY: 0.331 AC XY: 10723 AN XY: 32353

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.376

Alfa AF: 0.320 Hom.: 2322

Bravo AF: 0.362

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.2
Dann	Benign	0.73

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

Publications

LitVar

Other links and lift over

dbSNP: rs1927232; hg19: chrX-67382891;