22-35761250-CTGCTGCATCAT-C

Variant names:

• chr22-35761250-CTGCTGCATCAT-C
• NM_001349999.2:c.905_915delATGATGCAGCA

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1 PM2

The NM_001349999.2(RBFOX2):​c.905_915delATGATGCAGCA​(p.Asn302SerfsTer72) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RBFOX2 NM_001349999.2 frameshift
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.35

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

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBFOX2	NM_001349999.2	c.905_915delATGATGCAGCA	p.Asn302SerfsTer72	frameshift_variant	Exon 9 of 14	ENST00000695854.1	NP_001336928.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBFOX2	ENST00000695854.1	c.905_915delATGATGCAGCA	p.Asn302SerfsTer72	frameshift_variant	Exon 9 of 14		NM_001349999.2	ENSP00000512219.1
RBFOX2	ENST00000438146.7	c.905_915delATGATGCAGCA	p.Asn302SerfsTer76	frameshift_variant	Exon 9 of 14	1		ENSP00000413035.2
RBFOX2	ENST00000449924.6	c.692_702delATGATGCAGCA	p.Asn231SerfsTer76	frameshift_variant	Exon 8 of 13	1		ENSP00000391670.2
RBFOX2	ENST00000414461.6	c.692_702delATGATGCAGCA	p.Asn231SerfsTer134	frameshift_variant	Exon 8 of 12	1		ENSP00000407855.2
RBFOX2	ENST00000695805.1	n.*226_*236delATGATGCAGCA		non_coding_transcript_exon_variant	Exon 9 of 13			ENSP00000512185.1
RBFOX2	ENST00000695807.1	n.*145_*155delATGATGCAGCA		non_coding_transcript_exon_variant	Exon 9 of 15			ENSP00000512187.1
RBFOX2	ENST00000695805.1	n.*226_*236delATGATGCAGCA		3_prime_UTR_variant	Exon 9 of 13			ENSP00000512185.1
RBFOX2	ENST00000695807.1	n.*145_*155delATGATGCAGCA		3_prime_UTR_variant	Exon 9 of 15			ENSP00000512187.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Nov 28, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with RBFOX2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asn302Serfs*76) in the RBFOX2 gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in RBFOX2 cause disease. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr22-36157297;