7-99968196-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001185.4(AZGP1):c.572G>A(p.Arg191Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R191W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001185.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AZGP1 | NM_001185.4 | c.572G>A | p.Arg191Gln | missense_variant | Exon 3 of 4 | ENST00000292401.9 | NP_001176.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AZGP1 | ENST00000292401.9 | c.572G>A | p.Arg191Gln | missense_variant | Exon 3 of 4 | 1 | NM_001185.4 | ENSP00000292401.4 | ||
AZGP1 | ENST00000411734.1 | c.563G>A | p.Arg188Gln | missense_variant | Exon 3 of 3 | 1 | ENSP00000396093.1 | |||
AZGP1 | ENST00000419575.1 | c.139-19G>A | intron_variant | Intron 1 of 2 | 3 | ENSP00000389942.1 | ||||
AZGP1 | ENST00000477251.1 | n.568G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151762Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251220Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135844
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461888Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 727248
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151880Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74230
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at