16-7575790-A-G

Variant summary

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

The NM_018723.4(RBFOX1):c.271-3987A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,858 control chromosomes in the GnomAD database, including 25,083 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 0.57 (25083 hom., cov: 32)
• Consequence: RBFOX1 NM_018723.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.801

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBFOX1	NM_018723.4	c.271-3987A>G		intron_variant		ENST00000550418.6
RBFOX1	NM_145893.3	c.331-3987A>G		intron_variant		ENST00000355637.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBFOX1	ENST00000355637.9	c.331-3987A>G		intron_variant		1	NM_145893.3
RBFOX1	ENST00000550418.6	c.271-3987A>G		intron_variant		1	NM_018723.4	A1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86555 AN: 151740 Hom.: 25030 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.571 AC: 86662 AN: 151858 Hom.: 25083 Cov.: 32 AF XY: 0.568 AC XY: 42184 AN XY: 74218

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.591

Alfa AF: 0.535 Hom.: 28685

Bravo AF: 0.577

Asia WGS AF: 0.638 AC: 2217 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	5.0
Dann	Benign	0.14

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

Publications

LitVar

Other links and lift over

dbSNP: rs7191721; hg19: chr16-7625792;