GeneBe

rs193922937

Variant names:

Variant summary

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

The NM_002025.4(AFF2):​c.-455_-414delCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. 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)

Consequence

AFF2
NM_002025.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.80

Publications

1 publications found
Variant links:
Genes affected
AFF2 (HGNC:3776): (ALF transcription elongation factor 2) This gene encodes a putative transcriptional activator that is a member of the AF4\FMR2 gene family. This gene is associated with the folate-sensitive fragile X E locus on chromosome X. A repeat polymorphism in the fragile X E locus results in silencing of this gene causing Fragile X E syndrome. Fragile X E syndrome is a form of nonsyndromic X-linked cognitive disability. In addition, this gene contains 6-25 GCC repeats that are expanded to >200 repeats in the disease state. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jul 2016]
AFF2 Gene-Disease associations (from GenCC):
  • FRAXE intellectual disability
    Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae)
  • non-syndromic X-linked intellectual disability
    Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen

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ACMG classification

Classification was made for transcript

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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AFF2NM_002025.4 linkc.-455_-414delCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGC 5_prime_UTR_variant Exon 1 of 21 ENST00000370460.7 NP_002016.2 P51816-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AFF2ENST00000370460.7 linkc.-455_-414delCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGC 5_prime_UTR_variant Exon 1 of 21 5 NM_002025.4 ENSP00000359489.2 P51816-1
AFF2ENST00000342251.7 linkc.-460_-419delGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC upstream_gene_variant 1 ENSP00000345459.4 P51816-3
ENSG00000237741ENST00000456981.1 linkn.-64_-23delGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC upstream_gene_variant 3

Frequencies

GnomAD3 genomes
Cov.:
0
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.00
Hom.:
154
Bravo
AF:
0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
2.8

Splicing

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

Publications

Other links and lift over

dbSNP: rs193922937; hg19: chrX-147582157; API