rs10521254

chr16-6608054-T-C

Variant summary

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

The NM_018723.4(RBFOX1):c.-63-46549T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 152,204 control chromosomes in the GnomAD database, including 905 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 0.068 (905 hom., cov: 32)
• Consequence: RBFOX1 NM_018723.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBFOX1	NM_018723.4	c.-63-46549T>C		intron_variant		ENST00000550418.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBFOX1	ENST00000550418.6	c.-63-46549T>C		intron_variant		1	NM_018723.4	A1

Frequencies

GnomAD3 genomes AF: 0.0682 AC: 10375 AN: 152084 Hom.: 911 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.00684

Gnomad OTH AF: 0.0560

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

GnomAD4 genome AF: 0.0682 AC: 10381 AN: 152204 Hom.: 905 Cov.: 32 AF XY: 0.0718 AC XY: 5343 AN XY: 74430

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0356

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.00684

Gnomad4 OTH AF: 0.0550

Alfa AF: 0.0398 Hom.: 56

Bravo AF: 0.0724

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.47
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521254; hg19: chr16-6658055;