chrX-148500637-TGCCGCCGCCGCCGCCGCCGCCGCC-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_002025.4(AFF2):c.-437_-414del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., 20 hem., cov: 0)
Exomes 𝑓: 0.0016 ( 0 hom. 1 hem. )
Failed GnomAD Quality Control
Consequence
AFF2
NM_002025.4 5_prime_UTR
NM_002025.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.80
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant X-148500637-TGCCGCCGCCGCCGCCGCCGCCGCC-T is Benign according to our data. Variant chrX-148500637-TGCCGCCGCCGCCGCCGCCGCCGCC-T is described in ClinVar as [Likely_benign]. Clinvar id is 2661597.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00123 (90/73131) while in subpopulation AMR AF= 0.00405 (27/6668). AF 95% confidence interval is 0.00286. There are 0 homozygotes in gnomad4. There are 20 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
?
High Hemizygotes in GnomAd at 20 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AFF2 | NM_002025.4 | c.-437_-414del | 5_prime_UTR_variant | 1/21 | ENST00000370460.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFF2 | ENST00000370460.7 | c.-437_-414del | 5_prime_UTR_variant | 1/21 | 5 | NM_002025.4 | P1 | ||
AFF2 | ENST00000342251.7 | upstream_gene_variant | 1 | ||||||
ENST00000456981.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00122 AC: 89AN: 73146Hom.: 0 Cov.: 0 AF XY: 0.00129 AC XY: 20AN XY: 15462
GnomAD3 genomes
?
AF:
AC:
89
AN:
73146
Hom.:
Cov.:
0
AF XY:
AC XY:
20
AN XY:
15462
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00163 AC: 1AN: 614Hom.: 0 AF XY: 0.00610 AC XY: 1AN XY: 164
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
614
Hom.:
AF XY:
AC XY:
1
AN XY:
164
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00123 AC: 90AN: 73131Hom.: 0 Cov.: 0 AF XY: 0.00129 AC XY: 20AN XY: 15473
GnomAD4 genome
?
AF:
AC:
90
AN:
73131
Hom.:
Cov.:
0
AF XY:
AC XY:
20
AN XY:
15473
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | AFF2: BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at