chr19-11877700-G-A

Variant names:

• chr19-11877700-G-A
• rs11085795
• ENST00000592534.1:n.120-5851G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592534.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF439	ENST00000592534.1	TSL:3	n.120-5851G>A		intron	N/A

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

African (AFR) AF: 0.0474 AC: 1969 AN: 41514

American (AMR) AF: 0.196 AC: 2991 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3470

East Asian (EAS) AF: 0.00734 AC: 38 AN: 5180

South Asian (SAS) AF: 0.0929 AC: 448 AN: 4820

European-Finnish (FIN) AF: 0.293 AC: 3098 AN: 10556

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18442 AN: 67972

Other (OTH) AF: 0.163 AC: 344 AN: 2108

Alfa AF: 0.222 Hom.: 556

Bravo AF: 0.175

Asia WGS AF: 0.0480 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.37
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs11085795; hg19: chr19-11988515;