X-68212079-C-A

Variant names:

• chrX-68212079-C-A
• rs3788859
• NM_002547.3:c.702+29G>T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BS2_Supporting

The NM_002547.3(OPHN1):​c.702+29G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000324 in 925,107 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 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: not found (cov: 23)
  • Exomes 𝑓: 0.0000032 (0 hom. 2 hem.)
• Consequence: OPHN1 NM_002547.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847
• Publications: 0 publications found

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]

OPHN1 Gene-Disease associations (from GenCC):

• X-linked intellectual disability-cerebellar hypoplasia syndrome

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS2: High Hemizygotes in GnomAdExome4 at 2 XL geneVariant has number of hemizygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002547.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPHN1	NM_002547.3	MANE Select	c.702+29G>T		intron	N/A	NP_002538.1
	OPHN1	NM_001437258.1		c.702+29G>T		intron	N/A	NP_001424187.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPHN1	ENST00000355520.6	TSL:1 MANE Select	c.702+29G>T		intron	N/A	ENSP00000347710.5
	OPHN1	ENST00000905069.1		c.702+29G>T		intron	N/A	ENSP00000575128.1
	OPHN1	ENST00000681408.1		c.597+1783G>T		intron	N/A	ENSP00000506619.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 0.00000324 AC: 3 AN: 925107 Hom.: 0 Cov.: 15 AF XY: 0.00000771 AC XY: 2 AN XY: 259325

African (AFR) AF: 0.00 AC: 0 AN: 22908

American (AMR) AF: 0.00 AC: 0 AN: 32419

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17921

East Asian (EAS) AF: 0.00 AC: 0 AN: 28675

South Asian (SAS) AF: 0.00 AC: 0 AN: 48307

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39312

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3814

European-Non Finnish (NFE) AF: 0.00000434 AC: 3 AN: 691322

Other (OTH) AF: 0.00 AC: 0 AN: 40429

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.90
DANN	Benign	0.56
PhyloP100		0.85

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

Other links and lift over

dbSNP: rs3788859; hg19: chrX-67431921;