16-6910689-C-T

Variant summary

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

The NM_018723.4(RBFOX1):c.-15-141368C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,102 control chromosomes in the GnomAD database, including 40,895 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 0.73 (40895 hom., cov: 33)
• Consequence: RBFOX1 NM_018723.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBFOX1	NM_018723.4	c.-15-141368C>T		intron_variant		ENST00000550418.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBFOX1	ENST00000550418.6	c.-15-141368C>T		intron_variant		1	NM_018723.4	A1

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111100 AN: 151984 Hom.: 40849 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.731 AC: 111202 AN: 152102 Hom.: 40895 Cov.: 33 AF XY: 0.730 AC XY: 54261 AN XY: 74334

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.725

Alfa AF: 0.665 Hom.: 1919

Bravo AF: 0.739

Asia WGS AF: 0.861 AC: 2994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.2
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8057643; hg19: chr16-6960690;