7-99985596-C-T

Variant names:

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

Variant summary

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

The ENST00000686613.1(AZGP1P1):​n.359-194C>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 ENST00000686613.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

Genes affected

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

AZGP1P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AZGP1P1	ENST00000411909.1	n.349-177C>T		intron_variant	Intron 2 of 3	6
AZGP1P1	ENST00000686613.1	n.359-194C>T		intron_variant	Intron 2 of 3
AZGP1P1	ENST00000693057.2	n.363-1662C>T		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.972

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.964

Gnomad4 FIN AF: 0.971

Gnomad4 NFE AF: 0.958

Gnomad4 OTH AF: 0.947

Alfa AF: 0.954 Hom.: 12437

Bravo AF: 0.950

Asia WGS AF: 0.964 AC: 3350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6960542; hg19: chr7-99583219;