rs12158565

chr22-35920795-C-G

Variant summary

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

The NM_001349999.2(RBFOX2):c.237+18052G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,092 control chromosomes in the GnomAD database, including 5,456 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 0.22 (5456 hom., cov: 32)
• Consequence: RBFOX2 NM_001349999.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938

Genes affected

RBFOX2 (HGNC:9906): (RNA binding fox-1 homolog 2) This gene is one of several human genes similar to the C. elegans gene Fox-1. This gene encodes an RNA binding protein that is thought to be a key regulator of alternative exon splicing in the nervous system and other cell types. The protein binds to a conserved UGCAUG element found downstream of many alternatively spliced exons and promotes inclusion of the alternative exon in mature transcripts. The protein also interacts with the estrogen receptor 1 transcription factor and regulates estrogen receptor 1 transcriptional activity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBFOX2	NM_001349999.2	c.237+18052G>C		intron_variant		ENST00000695854.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBFOX2	ENST00000695854.1	c.237+18052G>C		intron_variant			NM_001349999.2	P3

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32902 AN: 151974 Hom.: 5425 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0781

Gnomad SAS AF: 0.0987

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.217 AC: 32991 AN: 152092 Hom.: 5456 Cov.: 32 AF XY: 0.210 AC XY: 15592 AN XY: 74340

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0782

Gnomad4 SAS AF: 0.0992

Gnomad4 FIN AF: 0.0999

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.183

Alfa AF: 0.183 Hom.: 468

Bravo AF: 0.230

Asia WGS AF: 0.108 AC: 378 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.23
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12158565; hg19: chr22-36316843;