16-6001142-C-T

Position:

• chr16-6001142-C-T

Variant summary

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

The NM_001415887.1(RBFOX1):​c.471+133807C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,192 control chromosomes in the GnomAD database, including 55,557 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 0.85 (55557 hom., cov: 32)
• Consequence: RBFOX1 NM_001415887.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBFOX1	NM_001415887.1	c.471+133807C>T		intron_variant			NP_001402816.1
RBFOX1	NM_001415888.1	c.471+133807C>T		intron_variant			NP_001402817.1
RBFOX1	XM_017023318.3	c.471+133807C>T		intron_variant			XP_016878807.1
RBFOX1	XM_024450303.2	c.432+133807C>T		intron_variant			XP_024306071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBFOX1	ENST00000641259.1	c.351+133807C>T		intron_variant				ENSP00000493041.1
RBFOX1	ENST00000569895.3	n.436+133807C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129263 AN: 152074 Hom.: 55504 Cov.: 32

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.850 AC: 129375 AN: 152192 Hom.: 55557 Cov.: 32 AF XY: 0.848 AC XY: 63056 AN XY: 74396

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.848

Alfa AF: 0.819 Hom.: 23794

Bravo AF: 0.857

Asia WGS AF: 0.945 AC: 3286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.56
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2059273; hg19: chr16-6051143;