rs308097
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_023382.1(ZNF815P):n.593G>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 0.0464 in 456,478 control chromosomes in the GnomAD database, including 746 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 0.035 ( 137 hom., cov: 32)
Exomes 𝑓: 0.052 ( 609 hom. )
Consequence
ZNF815P
NR_023382.1 non_coding_transcript_exon
NR_023382.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.70
Genes affected
ZNF815P (HGNC:22029): (zinc finger protein 815, pseudogene)
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.07).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF815P | NR_023382.1 | n.593G>A | non_coding_transcript_exon_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF815P | ENST00000434898.6 | n.649G>A | non_coding_transcript_exon_variant | 5/6 | |||||
ENST00000686456.1 | n.625G>A | non_coding_transcript_exon_variant | 4/5 |
Frequencies
GnomAD3 genomes ? AF: 0.0347 AC: 5273AN: 152068Hom.: 137 Cov.: 32
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GnomAD4 exome AF: 0.0524 AC: 15935AN: 304292Hom.: 609 Cov.: 0 AF XY: 0.0586 AC XY: 10152AN XY: 173286
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GnomAD4 genome ? AF: 0.0346 AC: 5268AN: 152186Hom.: 137 Cov.: 32 AF XY: 0.0338 AC XY: 2513AN XY: 74402
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at