chr16-6696744-C-A

Variant names:

• chr16-6696744-C-A
• rs1544616
• NM_018723.4:c.-16+42094C>A

Variant summary

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

The NM_018723.4(RBFOX1):​c.-16+42094C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.087 in 151,980 control chromosomes in the GnomAD database, including 1,070 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 0.087 (1070 hom., cov: 33)
• Consequence: RBFOX1 NM_018723.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 3 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=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018723.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBFOX1	NM_018723.4	MANE Select	c.-16+42094C>A		intron	N/A	NP_061193.2
	RBFOX1	NM_001415887.1		c.582+42094C>A		intron	N/A	NP_001402816.1
	RBFOX1	NM_001415888.1		c.582+42094C>A		intron	N/A	NP_001402817.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBFOX1	ENST00000550418.6	TSL:1 MANE Select	c.-16+42094C>A		intron	N/A	ENSP00000450031.1
	RBFOX1	ENST00000553186.5	TSL:1	c.-16+42094C>A		intron	N/A	ENSP00000447753.1
	RBFOX1	ENST00000551752.5	TSL:1	c.-16+42094C>A		intron	N/A	ENSP00000447281.1

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13208 AN: 151862 Hom.: 1069 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0305

Gnomad OTH AF: 0.0705

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

GnomAD4 genome AF: 0.0870 AC: 13220 AN: 151980 Hom.: 1070 Cov.: 33 AF XY: 0.0888 AC XY: 6594 AN XY: 74256

African (AFR) AF: 0.155 AC: 6413 AN: 41430

American (AMR) AF: 0.109 AC: 1665 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3472

East Asian (EAS) AF: 0.378 AC: 1957 AN: 5172

South Asian (SAS) AF: 0.120 AC: 579 AN: 4810

European-Finnish (FIN) AF: 0.0208 AC: 219 AN: 10520

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0305 AC: 2076 AN: 67990

Other (OTH) AF: 0.0712 AC: 150 AN: 2106

Alfa AF: 0.0488 Hom.: 1689

Bravo AF: 0.0971

Asia WGS AF: 0.226 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.51
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1544616; hg19: chr16-6746745;