3-28338611-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022461.5(AZI2):āc.221T>Gā(p.Ile74Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000703 in 1,607,752 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_022461.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AZI2 | NM_022461.5 | c.221T>G | p.Ile74Arg | missense_variant | 3/8 | ENST00000479665.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AZI2 | ENST00000479665.6 | c.221T>G | p.Ile74Arg | missense_variant | 3/8 | 2 | NM_022461.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152150Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000168 AC: 42AN: 249546Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 134986
GnomAD4 exome AF: 0.0000495 AC: 72AN: 1455602Hom.: 0 Cov.: 30 AF XY: 0.0000456 AC XY: 33AN XY: 723916
GnomAD4 genome AF: 0.000269 AC: 41AN: 152150Hom.: 1 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.221T>G (p.I74R) alteration is located in exon 3 (coding exon 2) of the AZI2 gene. This alteration results from a T to G substitution at nucleotide position 221, causing the isoleucine (I) at amino acid position 74 to be replaced by an arginine (R). 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