rs11085795

Variant names:

• chr19-11877700-G-A
• rs11085795
• ENST00000592534.1:n.120-5851G>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF439	ENST00000592534.1	n.120-5851G>A		intron_variant	Intron 1 of 1	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;