rs4508518
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001321645.3(ZNF224):āc.1107A>Gā(p.Glu369=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 1,582,610 control chromosomes in the GnomAD database, including 505,767 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: š 0.74 ( 42217 hom., cov: 32)
Exomes š: 0.80 ( 463550 hom. )
Consequence
ZNF224
NM_001321645.3 synonymous
NM_001321645.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.499
Genes affected
ZNF224 (HGNC:13017): (zinc finger protein 224) This gene encodes a member of the Krueppel C2H2-type zinc-finger family of proteins. The encoded protein represses transcription of the aldolase A gene, which encodes a key enzyme in glycolysis. The encoded zinc-finger protein may also function as a transcriptional co-activator with Wilms' tumor protein 1 to regulate apoptotic genes in leukemia. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP7
?
Synonymous conserved (PhyloP=-0.499 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF224 | NM_001321645.3 | c.1107A>G | p.Glu369= | synonymous_variant | 6/6 | ENST00000693561.1 | |
ZNF225-AS1 | NR_033341.1 | n.1433T>C | non_coding_transcript_exon_variant | 2/2 | |||
ZNF224 | NM_013398.5 | c.1107A>G | p.Glu369= | synonymous_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF224 | ENST00000693561.1 | c.1107A>G | p.Glu369= | synonymous_variant | 6/6 | NM_001321645.3 | P1 | ||
ZNF225-AS1 | ENST00000661725.1 | n.1433T>C | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.738 AC: 112122AN: 151950Hom.: 42190 Cov.: 32
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GnomAD3 exomes AF: 0.721 AC: 161962AN: 224612Hom.: 60413 AF XY: 0.731 AC XY: 88293AN XY: 120754
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GnomAD4 exome AF: 0.800 AC: 1144390AN: 1430542Hom.: 463550 Cov.: 82 AF XY: 0.799 AC XY: 566429AN XY: 709310
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GnomAD4 genome ? AF: 0.738 AC: 112189AN: 152068Hom.: 42217 Cov.: 32 AF XY: 0.727 AC XY: 53997AN XY: 74322
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at