chr19-44327931-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_013380.4(ZNF112):c.2226G>A(p.Pro742=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00163 in 1,609,758 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0089 ( 20 hom., cov: 32)
Exomes 𝑓: 0.00089 ( 18 hom. )
Consequence
ZNF112
NM_013380.4 synonymous
NM_013380.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.57
Genes affected
ZNF112 (HGNC:12892): (zinc finger protein 112) Predicted to enable DNA-binding transcription activator 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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
?
Variant 19-44327931-C-T is Benign according to our data. Variant chr19-44327931-C-T is described in ClinVar as [Benign]. Clinvar id is 769019.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.57 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00887 (1312/147982) while in subpopulation AFR AF= 0.0307 (1232/40124). AF 95% confidence interval is 0.0293. There are 20 homozygotes in gnomad4. There are 628 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 20 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF112 | NM_013380.4 | c.2226G>A | p.Pro742= | synonymous_variant | 4/4 | ENST00000354340.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF112 | ENST00000354340.9 | c.2226G>A | p.Pro742= | synonymous_variant | 4/4 | 1 | NM_013380.4 | A2 | |
ZNF112 | ENST00000337401.8 | c.2244G>A | p.Pro748= | synonymous_variant | 5/5 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00885 AC: 1308AN: 147858Hom.: 20 Cov.: 32
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GnomAD3 exomes AF: 0.00212 AC: 531AN: 250972Hom.: 7 AF XY: 0.00163 AC XY: 221AN XY: 135620
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GnomAD4 exome AF: 0.000895 AC: 1308AN: 1461776Hom.: 18 Cov.: 31 AF XY: 0.000796 AC XY: 579AN XY: 727192
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GnomAD4 genome ? AF: 0.00887 AC: 1312AN: 147982Hom.: 20 Cov.: 32 AF XY: 0.00868 AC XY: 628AN XY: 72330
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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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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at