rs3841049

chr14-21092593-GGAGGCTGAGGCT-Gchr14-21092593-GGAGGCTGAGGCT-GGAGGCTchr14-21092593-GGAGGCTGAGGCT-GGAGGCTGAGGCTGAGGCTchr14-21092593-GGAGGCTGAGGCT-GGAGGCTGAGGCTGAGGCTGAGGCT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

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
• 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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

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

GnomAD4 exome AF: 0.00000788 AC: 11 AN: 1395756 Hom.: 0 AF XY: 0.00000871 AC XY: 6 AN XY: 688730

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000280

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000926

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 28

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3841049; hg19: chr14-21560752;