rs375706788

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001185.4(AZGP1):​c.436G>T​(p.Glu146*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,888 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

AZGP1
NM_001185.4 stop_gained

Scores

1
6

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.851
Variant links:
Genes affected
AZGP1 (HGNC:910): (alpha-2-glycoprotein 1, zinc-binding) Involved in cell adhesion and detection of chemical stimulus involved in sensory perception of bitter taste. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AZGP1NM_001185.4 linkc.436G>T p.Glu146* stop_gained Exon 3 of 4 ENST00000292401.9 NP_001176.1 P25311A0A140VK00

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AZGP1ENST00000292401.9 linkc.436G>T p.Glu146* stop_gained Exon 3 of 4 1 NM_001185.4 ENSP00000292401.4 P25311
AZGP1ENST00000411734.1 linkc.427G>T p.Glu143* stop_gained Exon 3 of 3 1 ENSP00000396093.1 C9JEV0
AZGP1ENST00000419575.1 linkc.139-155G>T intron_variant Intron 1 of 2 3 ENSP00000389942.1 H7BZJ8
AZGP1ENST00000477251.1 linkn.432G>T non_coding_transcript_exon_variant Exon 1 of 2 2

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461888
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
727246
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.085
D
BayesDel_noAF
Benign
-0.11
CADD
Pathogenic
27
DANN
Benign
0.93
Eigen
Benign
-0.20
Eigen_PC
Benign
-0.62
FATHMM_MKL
Benign
0.017
N
Vest4
0.74
GERP RS
-0.25

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.090
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-99565955; API