ENST00000425474.6:n.-176A>G

Variant names:

• chr7-99980576-A-G
• rs2525557
• ENST00000425474.6:n.-176A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000425474.6(AZGP1P1):​n.-176A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.971 in 152,344 control chromosomes in the GnomAD database, including 71,763 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 0.97 (71763 hom., cov: 33)
• Consequence: AZGP1P1 ENST00000425474.6 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 5 publications found

Genes affected

AZGP1P1 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425474.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AZGP1P1	NR_036679.1		n.-186A>G		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AZGP1P1	ENST00000425474.6	TSL:1	n.-176A>G		upstream_gene	N/A
	AZGP1P1	ENST00000411909.1	TSL:6	n.-186A>G		upstream_gene	N/A
	AZGP1P1	ENST00000686613.2		n.-176A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.971 AC: 147739 AN: 152226 Hom.: 71704 Cov.: 33

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.979

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.965

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.971 AC: 147858 AN: 152344 Hom.: 71763 Cov.: 33 AF XY: 0.971 AC XY: 72350 AN XY: 74494

African (AFR) AF: 0.991 AC: 41181 AN: 41572

American (AMR) AF: 0.963 AC: 14736 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.973 AC: 3377 AN: 3472

East Asian (EAS) AF: 0.967 AC: 5010 AN: 5182

South Asian (SAS) AF: 0.965 AC: 4661 AN: 4828

European-Finnish (FIN) AF: 0.979 AC: 10401 AN: 10624

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.959 AC: 65283 AN: 68042

Other (OTH) AF: 0.965 AC: 2040 AN: 2114

Alfa AF: 0.964 Hom.: 191345

Bravo AF: 0.970

Asia WGS AF: 0.972 AC: 3382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2525557; hg19: chr7-99578199;