rs12982980
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001008801.2(ZNF468):c.142+2490G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 156,010 control chromosomes in the GnomAD database, including 9,994 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 0.32 ( 9994 hom., cov: 33)
Exomes 𝑓: 0.016 ( 0 hom. )
Consequence
ZNF468
NM_001008801.2 intron
NM_001008801.2 intron
Scores
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.624
Genes affected
ZNF468 (HGNC:33105): (zinc finger protein 468) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
ZNF28 (HGNC:13073): (zinc finger protein 28) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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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 (MetaRNN=1.8554392E-5).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF468 | NM_001008801.2 | c.142+2490G>A | intron_variant | ENST00000595646.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF468 | ENST00000595646.6 | c.142+2490G>A | intron_variant | 1 | NM_001008801.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.320 AC: 48657AN: 152008Hom.: 9999 Cov.: 33
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GnomAD3 exomes AF: 0.591 AC: 13AN: 22Hom.: 5 AF XY: 0.750 AC XY: 3AN XY: 4
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GnomAD4 exome AF: 0.0157 AC: 61AN: 3888Hom.: 0 Cov.: 0 AF XY: 0.0164 AC XY: 31AN XY: 1890
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GnomAD4 genome AF: 0.320 AC: 48637AN: 152122Hom.: 9994 Cov.: 33 AF XY: 0.315 AC XY: 23388AN XY: 74350
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ClinVar
Not reported inComputational scores
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BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MutationTaster
Benign
P;P;P
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at