18-59267631-GC-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_013435.3(RAX):c.*1372del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.11 (531 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: RAX NM_013435.3 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.510

Genes affected

RAX (HGNC:18662): (retina and anterior neural fold homeobox) This gene encodes a homeobox-containing transcription factor that functions in eye development. The gene is expressed early in the eye primordia, and is required for retinal cell fate determination and also regulates stem cell proliferation. Mutations in this gene have been reported in patients with defects in ocular development, including microphthalmia, anophthalmia, and coloboma.[provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAX	NM_013435.3	c.*1372del		3_prime_UTR_variant	3/3	ENST00000334889.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAX	ENST00000334889.4	c.*1372del		3_prime_UTR_variant	3/3	1	NM_013435.3	P1
RAX	ENST00000256852.7	c.*1844del		3_prime_UTR_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 9488 AN: 88338 Hom.: 527 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0894

Gnomad AMR AF: 0.0995

Gnomad ASJ AF: 0.0371

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0217

Gnomad NFE AF: 0.0796

Gnomad OTH AF: 0.0900

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.108 AC: 9502 AN: 88354 Hom.: 531 Cov.: 0 AF XY: 0.110 AC XY: 4483 AN XY: 40662

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0371

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.0799

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0795

Gnomad4 OTH AF: 0.0913

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Anophthalmia-microphthalmia syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

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: rs543386393; hg19: chr18-56934863;