rs9907432

Variant names:

• chr17-79144290-G-A
• rs9907432
• NM_001350451.2:c.-33-28542C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001350451.2(RBFOX3):​c.-33-28542C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,196 control chromosomes in the GnomAD database, including 4,953 homozygotes. 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 0.25 (4953 hom., cov: 34)
• Consequence: RBFOX3 NM_001350451.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 5 publications found

Genes affected

RBFOX3 (HGNC:27097): (RNA binding fox-1 homolog 3) This gene encodes a member of the RNA-binding FOX protein family which is involved in the regulation of alternative splicing of pre-mRNA. The protein has an N-terminal proline-rich region, an RNA recognition motif (RRM) domain, and a C-terminal alanine-rich region. This gene produces the neuronal nuclei (NeuN) antigen that has been widely used as a marker for post-mitotic neurons. This gene has its highest expression in the central nervous system and plays a prominent role in neural tissue development and regulation of adult brain function. Mutations in this gene have been associated with numerous neurological disorders. Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, May 2017]

RBFOX3 Gene-Disease associations (from GenCC):

• epilepsy

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350451.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBFOX3	NM_001350451.2	MANE Select	c.-33-28542C>T		intron	N/A	NP_001337380.1
	RBFOX3	NM_001385804.1		c.-33-28542C>T		intron	N/A	NP_001372733.1
	RBFOX3	NM_001385805.1		c.-33-28542C>T		intron	N/A	NP_001372734.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBFOX3	ENST00000693108.1	MANE Select	c.-33-28542C>T		intron	N/A	ENSP00000510395.1
	RBFOX3	ENST00000583458.5	TSL:5	c.-33-28542C>T		intron	N/A	ENSP00000464186.1
	RBFOX3	ENST00000582043.5	TSL:5	c.-33-28542C>T		intron	N/A	ENSP00000463964.1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37408 AN: 152078 Hom.: 4947 Cov.: 34

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.00615

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.246 AC: 37443 AN: 152196 Hom.: 4953 Cov.: 34 AF XY: 0.242 AC XY: 18002 AN XY: 74416

African (AFR) AF: 0.204 AC: 8459 AN: 41526

American (AMR) AF: 0.192 AC: 2931 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3470

East Asian (EAS) AF: 0.00636 AC: 33 AN: 5188

South Asian (SAS) AF: 0.172 AC: 833 AN: 4830

European-Finnish (FIN) AF: 0.263 AC: 2782 AN: 10584

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20827 AN: 67982

Other (OTH) AF: 0.250 AC: 528 AN: 2114

Alfa AF: 0.277 Hom.: 16670

Bravo AF: 0.236

Asia WGS AF: 0.0930 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.88
PhyloP100		-0.051
Mutation Taster		=100/0	polymorphism (auto)

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: rs9907432; hg19: chr17-77140372;