rs755428630
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM1PM4_SupportingBS2
The NM_014423.4(AFF4):c.516_518dupACA(p.Glu172_His173insGln) variant causes a disruptive inframe insertion change. The variant allele was found at a frequency of 0.0000192 in 1,614,158 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000021 ( 1 hom. )
Consequence
AFF4
NM_014423.4 disruptive_inframe_insertion
NM_014423.4 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.21
Genes affected
AFF4 (HGNC:17869): (ALF transcription elongation factor 4) The protein encoded by this gene belongs to the AF4 family of transcription factors involved in leukemia. It is a component of the positive transcription elongation factor b (P-TEFb) complex. A chromosomal translocation involving this gene and MLL gene on chromosome 11 is found in infant acute lymphoblastic leukemia with ins(5;11)(q31;q31q23). [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM1
In a region_of_interest Disordered (size 236) in uniprot entity AFF4_HUMAN there are 8 pathogenic changes around while only 1 benign (89%) in NM_014423.4
PM4
Nonframeshift variant in NON repetitive region in NM_014423.4. Strenght limited to Supporting due to length of the change: 1aa.
BS2
High AC in GnomAdExome4 at 30 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AFF4 | NM_014423.4 | c.516_518dupACA | p.Glu172_His173insGln | disruptive_inframe_insertion | Exon 3 of 21 | ENST00000265343.10 | NP_055238.1 | |
AFF4 | XM_005271963.6 | c.516_518dupACA | p.Glu172_His173insGln | disruptive_inframe_insertion | Exon 4 of 22 | XP_005272020.1 | ||
AFF4 | XM_006714587.5 | c.516_518dupACA | p.Glu172_His173insGln | disruptive_inframe_insertion | Exon 3 of 20 | XP_006714650.1 | ||
AFF4 | XM_047417103.1 | c.516_518dupACA | p.Glu172_His173insGln | disruptive_inframe_insertion | Exon 4 of 21 | XP_047273059.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AFF4 | ENST00000265343.10 | c.516_518dupACA | p.Glu172_His173insGln | disruptive_inframe_insertion | Exon 3 of 21 | 1 | NM_014423.4 | ENSP00000265343.5 | ||
AFF4 | ENST00000378595.7 | c.516_518dupACA | p.Glu172_His173insGln | disruptive_inframe_insertion | Exon 3 of 13 | 1 | ENSP00000367858.3 | |||
AFF4 | ENST00000465484.1 | n.775_777dupACA | non_coding_transcript_exon_variant | Exon 3 of 5 | 1 | |||||
AFF4 | ENST00000491831.5 | n.776_778dupACA | non_coding_transcript_exon_variant | Exon 3 of 7 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461890Hom.: 1 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727244
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74464
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, no assertion criteria provided | research | Gharavi Laboratory, Columbia University | Sep 16, 2018 | - - |
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 29, 2024 | This variant, c.516_518dup, results in the insertion of 1 amino acid(s) of the AFF4 protein (p.Glu172_His173insGln), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with AFF4-related conditions. ClinVar contains an entry for this variant (Variation ID: 591050). 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. - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at