GeneBe

rs55993073

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_213594.3(RFX4):​c.44-14_44-3delTTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000782 in 1,278,178 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 7.8e-7 ( 0 hom. )

Consequence

RFX4
NM_213594.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.07
Variant links:
Genes affected
RFX4 (HGNC:9985): (regulatory factor X4) This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X2, X3, and X5. It has been shown to interact with itself as well as with regulatory factors X2 and X3, but it does not interact with regulatory factor X1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RFX4NM_213594.3 linkc.44-14_44-3delTTTTTTTTTTTT splice_region_variant, intron_variant Intron 1 of 17 ENST00000392842.6 NP_998759.1 Q33E94-1
RFX4NM_001206691.2 linkc.71-14_71-3delTTTTTTTTTTTT splice_region_variant, intron_variant Intron 1 of 17 NP_001193620.1 Q33E94-2
LOC100287944NR_040246.1 linkn.143-100982_143-100971delAAAAAAAAAAAA intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RFX4ENST00000392842.6 linkc.44-16_44-5delTTTTTTTTTTTT splice_region_variant, intron_variant Intron 1 of 17 1 NM_213594.3 ENSP00000376585.1 Q33E94-1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
7.82e-7
AC:
1
AN:
1278178
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
636674
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000278
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: chr12-107002558; API