rs62057608
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000562068.2(ZNF971P):n.325G>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 0.0266 in 454,902 control chromosomes in the GnomAD database, including 242 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 0.026 ( 64 hom., cov: 34)
Exomes 𝑓: 0.027 ( 178 hom. )
Consequence
ZNF971P
ENST00000562068.2 non_coding_transcript_exon
ENST00000562068.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.47
Genes affected
ZNF971P (HGNC:51848): (zinc finger protein 971, 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=-0.72).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0259 (3939/152246) while in subpopulation NFE AF= 0.0401 (2724/68000). AF 95% confidence interval is 0.0388. There are 64 homozygotes in gnomad4. There are 1863 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 64 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF971P | ENST00000562068.2 | n.325G>A | non_coding_transcript_exon_variant | 1/1 | |||||
ENST00000568619.2 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0259 AC: 3939AN: 152128Hom.: 64 Cov.: 34
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0216 AC: 2981AN: 138018Hom.: 54 AF XY: 0.0207 AC XY: 1542AN XY: 74632
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GnomAD4 exome AF: 0.0269 AC: 8141AN: 302656Hom.: 178 Cov.: 0 AF XY: 0.0248 AC XY: 4273AN XY: 172262
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GnomAD4 genome ? AF: 0.0259 AC: 3939AN: 152246Hom.: 64 Cov.: 34 AF XY: 0.0250 AC XY: 1863AN XY: 74442
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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