ENST00000411909.1:n.349-177C>T

Variant names:

• chr7-99985596-C-T
• rs6960542
• ENST00000411909.1:n.349-177C>T

Variant summary

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

The ENST00000411909.1(AZGP1P1):​n.349-177C>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 ENST00000411909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 5 publications found

Genes affected

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

AZGP1P1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411909.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AZGP1P1	ENST00000411909.1	TSL:6	n.349-177C>T		intron	N/A
	AZGP1P1	ENST00000686613.2		n.359-194C>T		intron	N/A
	AZGP1P1	ENST00000693057.3		n.409-1662C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.952 AC: 144734 AN: 152092 Hom.: 68878 Cov.: 31

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

African (AFR) AF: 0.928 AC: 38517 AN: 41516

American (AMR) AF: 0.959 AC: 14664 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.972 AC: 3375 AN: 3472

East Asian (EAS) AF: 0.964 AC: 4967 AN: 5154

South Asian (SAS) AF: 0.964 AC: 4650 AN: 4822

European-Finnish (FIN) AF: 0.971 AC: 10294 AN: 10600

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

European-Non Finnish (NFE) AF: 0.958 AC: 65205 AN: 68030

Other (OTH) AF: 0.947 AC: 2004 AN: 2116

Alfa AF: 0.955 Hom.: 116289

Bravo AF: 0.950

Asia WGS AF: 0.964 AC: 3350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.57
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6960542; hg19: chr7-99583219;