dbSNP rs4729562: AZGP1P1:n.603G>A (chr7-99986027-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000686613.1(AZGP1P1):n.596G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 1,581,936 control chromosomes in the GnomAD database, including 372,311 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 0.71 ( 38098 hom., cov: 29)

Exomes 𝑓: 0.68 ( 334213 hom. )

Consequence

AZGP1P1
ENST00000686613.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.298

Variant links:

Genes affected

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

AZGP1P1 links:

AZGP1P1 (HGNC:):

AZGP1P1 links:

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
AZGP1P1	ENST00000411909.1 link	n.603G>A	non_coding_transcript_exon_variant	Exon 3 of 4	6
AZGP1P1	ENST00000686613.1 link	n.596G>A	non_coding_transcript_exon_variant	Exon 3 of 4
AZGP1P1	ENST00000701281.1 link	n.636G>A	non_coding_transcript_exon_variant	Exon 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.706

AC:

107084

AN:

151598

Hom.:

38059

Cov.:

show subpopulations

Gnomad AFR

AF:

0.768

Gnomad AMI

AF:

0.703

Gnomad AMR

AF:

0.758

Gnomad ASJ

AF:

0.730

Gnomad EAS

AF:

0.751

Gnomad SAS

AF:

0.668

Gnomad FIN

AF:

0.600

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.671

Gnomad OTH

AF:

0.721

GnomAD4 exome

AF:

0.682

AC:

975507

AN:

1430222

Hom.:

334213

Cov.:

AF XY:

0.682

AC XY:

486330

AN XY:

712838

show subpopulations

Gnomad4 AFR exome

AF:

0.778

Gnomad4 AMR exome

AF:

0.791

Gnomad4 ASJ exome

AF:

0.732

Gnomad4 EAS exome

AF:

0.754

Gnomad4 SAS exome

AF:

0.686

Gnomad4 FIN exome

AF:

0.608

Gnomad4 NFE exome

AF:

0.673

Gnomad4 OTH exome

AF:

0.701

GnomAD4 genome

AF:

0.706

AC:

107179

AN:

151714

Hom.:

38098

Cov.:

AF XY:

0.705

AC XY:

52225

AN XY:

74118

show subpopulations

Gnomad4 AFR

AF:

0.768

Gnomad4 AMR

AF:

0.758

Gnomad4 ASJ

AF:

0.730

Gnomad4 EAS

AF:

0.751

Gnomad4 SAS

AF:

0.669

Gnomad4 FIN

AF:

0.600

Gnomad4 NFE

AF:

0.671

Gnomad4 OTH

AF:

0.722

Alfa

AF:

0.669

Hom.:

5272

Bravo

AF:

0.723

Asia WGS

AF:

0.682

AC:

2369

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

7.7

DANN

Benign

0.56

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