rs4729562
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
ENST00000411909.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.298
Genes affected
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ACMG classification
Classification made for transcript
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 | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | 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: 107084AN: 151598Hom.: 38059 Cov.: 29
GnomAD3 genomes
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GnomAD4 exome AF: 0.682 AC: 975507AN: 1430222Hom.: 334213 Cov.: 32 AF XY: 0.682 AC XY: 486330AN XY: 712838
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GnomAD4 genome ? AF: 0.706 AC: 107179AN: 151714Hom.: 38098 Cov.: 29 AF XY: 0.705 AC XY: 52225AN XY: 74118
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at