7-99985596-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000686613.1(AZGP1P1):​n.359-194C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 152,210 control chromosomes in the GnomAD database, including 68,930 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.95 ( 68930 hom., cov: 31)

Consequence

AZGP1P1
ENST00000686613.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.19
Variant links:
Genes affected
AZGP1P1 (HGNC:911): (AZGP1 pseudogene 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
AZGP1P1ENST00000411909.1 linkn.349-177C>T intron_variant 6
AZGP1P1ENST00000686613.1 linkn.359-194C>T intron_variant
AZGP1P1ENST00000693057.2 linkn.363-1662C>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.952
AC:
144734
AN:
152092
Hom.:
68878
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.928
Gnomad AMI
AF:
0.981
Gnomad AMR
AF:
0.959
Gnomad ASJ
AF:
0.972
Gnomad EAS
AF:
0.964
Gnomad SAS
AF:
0.964
Gnomad FIN
AF:
0.971
Gnomad MID
AF:
0.937
Gnomad NFE
AF:
0.958
Gnomad OTH
AF:
0.947
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.952
AC:
144845
AN:
152210
Hom.:
68930
Cov.:
31
AF XY:
0.952
AC XY:
70864
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.928
Gnomad4 AMR
AF:
0.959
Gnomad4 ASJ
AF:
0.972
Gnomad4 EAS
AF:
0.964
Gnomad4 SAS
AF:
0.964
Gnomad4 FIN
AF:
0.971
Gnomad4 NFE
AF:
0.958
Gnomad4 OTH
AF:
0.947
Alfa
AF:
0.954
Hom.:
12437
Bravo
AF:
0.950
Asia WGS
AF:
0.964
AC:
3350
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.17
DANN
Benign
0.57

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6960542; hg19: chr7-99583219; API