rs201152809
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_002025.4(AFF2):c.561C>A(p.Asp187Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000421 in 1,210,003 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_002025.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AFF2 | NM_002025.4 | c.561C>A | p.Asp187Glu | missense_variant | 3/21 | ENST00000370460.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFF2 | ENST00000370460.7 | c.561C>A | p.Asp187Glu | missense_variant | 3/21 | 5 | NM_002025.4 | P1 | |
AFF2 | ENST00000342251.7 | c.549C>A | p.Asp183Glu | missense_variant | 3/20 | 1 | |||
AFF2 | ENST00000370457.9 | c.561C>A | p.Asp187Glu | missense_variant | 3/20 | 1 | |||
AFF2 | ENST00000370458.5 | c.549C>A | p.Asp183Glu | missense_variant | 3/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000537 AC: 6AN: 111770Hom.: 0 Cov.: 23 AF XY: 0.0000589 AC XY: 2AN XY: 33950
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 183428Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67872
GnomAD4 exome AF: 0.0000410 AC: 45AN: 1098233Hom.: 0 Cov.: 32 AF XY: 0.0000413 AC XY: 15AN XY: 363587
GnomAD4 genome ? AF: 0.0000537 AC: 6AN: 111770Hom.: 0 Cov.: 23 AF XY: 0.0000589 AC XY: 2AN XY: 33950
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 10, 2016 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2022 | The c.561C>A (p.D187E) alteration is located in exon 3 (coding exon 3) of the AFF2 gene. This alteration results from a C to A substitution at nucleotide position 561, causing the aspartic acid (D) at amino acid position 187 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at