chr19-44100937-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001321645.3(ZNF224):c.142+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00158 in 1,613,440 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0082 ( 25 hom., cov: 31)
Exomes 𝑓: 0.00089 ( 24 hom. )
Consequence
ZNF224
NM_001321645.3 intron
NM_001321645.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.420
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 19-44100937-G-A is Benign according to our data. Variant chr19-44100937-G-A is described in ClinVar as [Benign]. Clinvar id is 777498.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0082 (1248/152212) while in subpopulation AFR AF= 0.0288 (1197/41526). AF 95% confidence interval is 0.0275. There are 25 homozygotes in gnomad4. There are 556 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 25 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF224 | NM_001321645.3 | c.142+10G>A | intron_variant | ENST00000693561.1 | |||
ZNF224 | NM_013398.5 | c.142+10G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF224 | ENST00000693561.1 | c.142+10G>A | intron_variant | NM_001321645.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00817 AC: 1242AN: 152094Hom.: 24 Cov.: 31
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GnomAD3 exomes AF: 0.00214 AC: 535AN: 250576Hom.: 8 AF XY: 0.00148 AC XY: 200AN XY: 135432
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GnomAD4 exome AF: 0.000887 AC: 1296AN: 1461228Hom.: 24 Cov.: 65 AF XY: 0.000802 AC XY: 583AN XY: 726926
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GnomAD4 genome AF: 0.00820 AC: 1248AN: 152212Hom.: 25 Cov.: 31 AF XY: 0.00747 AC XY: 556AN XY: 74424
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 16, 2018 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at