rs870288

Variant names:

• chr16-5535851-A-G
• rs870288
• ENST00000641259.1:c.259-63051A>G

Variant summary

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

The ENST00000641259.1(RBFOX1):​c.259-63051A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,138 control chromosomes in the GnomAD database, including 8,700 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 0.31 (8700 hom., cov: 32)
• Consequence: RBFOX1 ENST00000641259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 11 publications found

Genes affected

RBFOX1 (HGNC:18222): (RNA binding fox-1 homolog 1) The Fox-1 family of RNA-binding proteins is evolutionarily conserved, and regulates tissue-specific alternative splicing in metazoa. Fox-1 recognizes a (U)GCAUG stretch in regulated exons or in flanking introns. The protein binds to the C-terminus of ataxin-2 and may contribute to the restricted pathology of spinocerebellar ataxia type 2 (SCA2). Ataxin-2 is the product of the SCA2 gene which causes familial neurodegenerative diseases. Fox-1 and ataxin-2 are both localized in the trans-Golgi network. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

RBFOX1 Gene-Disease associations (from GenCC):

• epilepsy

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: G2P
• autism susceptibility 1

  Inheritance: Unknown Classification: LIMITED Submitted by: Laboratory for Molecular Medicine

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBFOX1	NM_001415887.1	c.379-63051A>G		intron_variant	Intron 2 of 19		NP_001402816.1
RBFOX1	NM_001415888.1	c.379-63051A>G		intron_variant	Intron 2 of 17		NP_001402817.1
RBFOX1	XM_017023318.3	c.379-63051A>G		intron_variant	Intron 2 of 19		XP_016878807.1
RBFOX1	XM_024450303.2	c.340-63051A>G		intron_variant	Intron 1 of 18		XP_024306071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBFOX1	ENST00000641259.1	c.259-63051A>G		intron_variant	Intron 2 of 19			ENSP00000493041.1
RBFOX1	ENST00000585867.2	c.259-63051A>G		intron_variant	Intron 2 of 2	2		ENSP00000493140.1
RBFOX1	ENST00000569895.3	n.344-63051A>G		intron_variant	Intron 2 of 6	3

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47215 AN: 152020 Hom.: 8690 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.311 AC: 47249 AN: 152138 Hom.: 8700 Cov.: 32 AF XY: 0.319 AC XY: 23769 AN XY: 74402

African (AFR) AF: 0.209 AC: 8683 AN: 41492

American (AMR) AF: 0.362 AC: 5535 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1253 AN: 3472

East Asian (EAS) AF: 0.854 AC: 4425 AN: 5180

South Asian (SAS) AF: 0.597 AC: 2873 AN: 4814

European-Finnish (FIN) AF: 0.305 AC: 3227 AN: 10586

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20277 AN: 67986

Other (OTH) AF: 0.313 AC: 661 AN: 2112

Alfa AF: 0.312 Hom.: 36063

Bravo AF: 0.307

Asia WGS AF: 0.693 AC: 2408 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.65
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs870288; hg19: chr16-5585852;