rs4729562

Positions:

• chr7-99986027-G-A
• chr7-99986027-G-C
• chr7-99986027-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000411909.1(AZGP1P1):​n.603G>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 ENST00000411909.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

Genes affected

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

ACMG classification

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AZGP1P1	ENST00000411909.1	n.603G>A		non_coding_transcript_exon_variant	3/4
AZGP1P1	ENST00000701281.1	n.636G>A		non_coding_transcript_exon_variant	3/4

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

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.: 29 AF XY: 0.705 AC XY: 52225 AN XY: 74118

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

Other links and lift over

dbSNP: rs4729562; hg19: chr7-99583650;