chrX-148661960-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_002025.4(AFF2):āc.233A>Gā(p.Tyr78Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000912 in 1,206,601 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. Y78Y) has been classified as Likely benign.
Frequency
Consequence
NM_002025.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AFF2 | NM_002025.4 | c.233A>G | p.Tyr78Cys | missense_variant | 3/21 | ENST00000370460.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFF2 | ENST00000370460.7 | c.233A>G | p.Tyr78Cys | missense_variant | 3/21 | 5 | NM_002025.4 | P1 | |
AFF2 | ENST00000342251.7 | c.221A>G | p.Tyr74Cys | missense_variant | 3/20 | 1 | |||
AFF2 | ENST00000370457.9 | c.233A>G | p.Tyr78Cys | missense_variant | 3/20 | 1 | |||
AFF2 | ENST00000370458.5 | c.221A>G | p.Tyr74Cys | missense_variant | 3/8 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111748Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33916
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 182619Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67143
GnomAD4 exome AF: 0.00000822 AC: 9AN: 1094853Hom.: 0 Cov.: 30 AF XY: 0.00000555 AC XY: 2AN XY: 360383
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111748Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33916
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 07, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at