Variant 7-99985596-C-T details in Genebe, Genetics Data Aggregator

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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.19

Variant links:

Genes affected

AZGP1P1 (HGNC:911): (AZGP1 pseudogene 1)

AZGP1P1 links:

AZGP1P1 (HGNC:):

AZGP1P1 links:

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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	Effect	TSL
AZGP1P1	ENST00000411909.1 link	n.349-177C>T	intron_variant	6
AZGP1P1	ENST00000686613.1 link	n.359-194C>T	intron_variant
AZGP1P1	ENST00000693057.2 link	n.363-1662C>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.952

AC:

144734

AN:

152092

Hom.:

68878

Cov.:

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.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over