rs11085795

Positions:

• chr19-11877700-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000592534.1(ZNF439):​n.120-5851G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,088 control chromosomes in the GnomAD database, including 3,563 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (3563 hom., cov: 32)
• Consequence: ZNF439 ENST00000592534.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

ZNF439 (HGNC:20873): (zinc finger protein 439) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF439	ENST00000592534.1	n.120-5851G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28290 AN: 151970 Hom.: 3561 Cov.: 32

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.00732

Gnomad SAS AF: 0.0931

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.165

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.186 AC: 28291 AN: 152088 Hom.: 3563 Cov.: 32 AF XY: 0.185 AC XY: 13766 AN XY: 74340

Gnomad4 AFR AF: 0.0474

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.00734

Gnomad4 SAS AF: 0.0929

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.163

Alfa AF: 0.228 Hom.: 555

Bravo AF: 0.175

Asia WGS AF: 0.0480 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11085795; hg19: chr19-11988515;