chrX-148661970-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_002025.4(AFF2):c.243G>T(p.Met81Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000896 in 111,588 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic 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 Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AFF2 | NM_002025.4 | c.243G>T | p.Met81Ile | missense_variant | 3/21 | ENST00000370460.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFF2 | ENST00000370460.7 | c.243G>T | p.Met81Ile | missense_variant | 3/21 | 5 | NM_002025.4 | P1 | |
AFF2 | ENST00000342251.7 | c.231G>T | p.Met77Ile | missense_variant | 3/20 | 1 | |||
AFF2 | ENST00000370457.9 | c.243G>T | p.Met81Ile | missense_variant | 3/20 | 1 | |||
AFF2 | ENST00000370458.5 | c.231G>T | p.Met77Ile | missense_variant | 3/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000896 AC: 1AN: 111588Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33788
GnomAD3 exomes AF: 0.00000547 AC: 1AN: 182968Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67462
GnomAD4 exome Cov.: 30
GnomAD4 genome ? AF: 0.00000896 AC: 1AN: 111588Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33788
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 27, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at