rs3841049
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_016423.3(ZNF219):c.692_703del(p.Gln231_Pro234del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000788 in 1,395,756 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 28)
Exomes 𝑓: 0.0000079 ( 0 hom. )
Consequence
ZNF219
NM_016423.3 inframe_deletion
NM_016423.3 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.70
Genes affected
ZNF219 (HGNC:13011): (zinc finger protein 219) This gene is a member of the Kruppel-like zinc finger gene family. The encoded protein functions as a transcriptional repressor of the high mobility group nucleosome binding domain 1 protein, which is associated with transcriptionally active chromatin. [provided by RefSeq, Apr 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 11 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF219 | NM_016423.3 | c.692_703del | p.Gln231_Pro234del | inframe_deletion | 3/5 | ENST00000360947.8 | |
ZNF219 | NM_001101672.2 | c.692_703del | p.Gln231_Pro234del | inframe_deletion | 3/5 | ||
ZNF219 | NM_001102454.2 | c.692_703del | p.Gln231_Pro234del | inframe_deletion | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF219 | ENST00000360947.8 | c.692_703del | p.Gln231_Pro234del | inframe_deletion | 3/5 | 1 | NM_016423.3 | P1 | |
ZNF219 | ENST00000421093.6 | c.692_703del | p.Gln231_Pro234del | inframe_deletion | 3/5 | 1 | P1 | ||
ZNF219 | ENST00000451119.6 | c.692_703del | p.Gln231_Pro234del | inframe_deletion | 3/5 | 5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 28
GnomAD3 genomes
Cov.:
28
GnomAD4 exome AF: 0.00000788 AC: 11AN: 1395756Hom.: 0 AF XY: 0.00000871 AC XY: 6AN XY: 688730
GnomAD4 exome
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11
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1395756
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6
AN XY:
688730
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GnomAD4 genome Cov.: 28
GnomAD4 genome
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28
Bravo
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at