chr19-52374423-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001145434.2(ZNF880):c.264C>T(p.Asn88Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000297 in 1,610,690 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 1 hom., cov: 30)
Exomes 𝑓: 0.00021 ( 0 hom. )
Consequence
ZNF880
NM_001145434.2 synonymous
NM_001145434.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0950
Genes affected
ZNF880 (HGNC:37249): (zinc finger protein 880) 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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 19-52374423-C-T is Benign according to our data. Variant chr19-52374423-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2650391.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.095 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00116 AC: 175AN: 151300Hom.: 1 Cov.: 30
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GnomAD3 exomes AF: 0.000456 AC: 112AN: 245672Hom.: 0 AF XY: 0.000391 AC XY: 52AN XY: 132866
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GnomAD4 exome AF: 0.000208 AC: 303AN: 1459276Hom.: 0 Cov.: 31 AF XY: 0.000198 AC XY: 144AN XY: 725616
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GnomAD4 genome AF: 0.00116 AC: 175AN: 151414Hom.: 1 Cov.: 30 AF XY: 0.00119 AC XY: 88AN XY: 73934
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Oct 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
ZNF880: BP4, BP7 -
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