GeneBe

rs55993073

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

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. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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

Publications

0 publications found
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 was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_213594.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
RFX4
NM_213594.3
MANE Select
c.44-14_44-3delTTTTTTTTTTTT
splice_region intron
N/ANP_998759.1Q33E94-1
RFX4
NM_001206691.2
c.71-14_71-3delTTTTTTTTTTTT
splice_region intron
N/ANP_001193620.1Q33E94-2
LOC100287944
NR_040246.1
n.143-100982_143-100971delAAAAAAAAAAAA
intron
N/A

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
RFX4
ENST00000392842.6
TSL:1 MANE Select
c.44-16_44-5delTTTTTTTTTTTT
splice_region intron
N/AENSP00000376585.1Q33E94-1
RFX4
ENST00000357881.8
TSL:1
c.71-16_71-5delTTTTTTTTTTTT
splice_region intron
N/AENSP00000350552.4Q33E94-2
RFX4
ENST00000536688.5
TSL:1
n.176-16_176-5delTTTTTTTTTTTT
splice_region intron
N/A

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
African (AFR)
AF:
0.00
AC:
0
AN:
27610
American (AMR)
AF:
0.00
AC:
0
AN:
28692
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
22136
East Asian (EAS)
AF:
0.0000278
AC:
1
AN:
36020
South Asian (SAS)
AF:
0.00
AC:
0
AN:
70876
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
40814
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5068
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
993716
Other (OTH)
AF:
0.00
AC:
0
AN:
53246
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs55993073; hg19: chr12-107002558; API