chr7-99986027-G-A

Variant names:

• chr7-99986027-G-A
• rs4729562
• ENST00000411909.1:n.603G>A

Variant summary

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

The ENST00000686613.2(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 ENST00000686613.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 13 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000686613.2. 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.603G>A		non_coding_transcript_exon	Exon 3 of 4
	AZGP1P1	ENST00000686613.2		n.596G>A		non_coding_transcript_exon	Exon 3 of 4
	AZGP1P1	ENST00000701281.2		n.636G>A		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107084 AN: 151598 Hom.: 38059 Cov.: 29

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.: 32 AF XY: 0.682 AC XY: 486330 AN XY: 712838

African (AFR) AF: 0.778 AC: 25551 AN: 32860

American (AMR) AF: 0.791 AC: 35200 AN: 44508

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 18910 AN: 25830

East Asian (EAS) AF: 0.754 AC: 29806 AN: 39510

South Asian (SAS) AF: 0.686 AC: 58341 AN: 85106

European-Finnish (FIN) AF: 0.608 AC: 32132 AN: 52888

Middle Eastern (MID) AF: 0.757 AC: 3193 AN: 4218

European-Non Finnish (NFE) AF: 0.673 AC: 730810 AN: 1086010

Other (OTH) AF: 0.701 AC: 41564 AN: 59292

GnomAD4 genome AF: 0.706 AC: 107179 AN: 151714 Hom.: 38098 Cov.: 29 AF XY: 0.705 AC XY: 52225 AN XY: 74118

African (AFR) AF: 0.768 AC: 31780 AN: 41382

American (AMR) AF: 0.758 AC: 11528 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2530 AN: 3466

East Asian (EAS) AF: 0.751 AC: 3844 AN: 5118

South Asian (SAS) AF: 0.669 AC: 3221 AN: 4814

European-Finnish (FIN) AF: 0.600 AC: 6283 AN: 10468

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45618 AN: 67946

Other (OTH) AF: 0.722 AC: 1519 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.7
DANN	Benign	0.56
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs4729562; hg19: chr7-99583650;