chr19-56428202-G-A

Variant names:

• chr19-56428202-G-A
• rs8104319
• ENST00000585612.1:n.653+4400G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000585612.1(ZNF583):​n.653+4400G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,992 control chromosomes in the GnomAD database, including 24,633 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 0.56 (24633 hom., cov: 32)
• Consequence: ZNF583 ENST00000585612.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 4 publications found

Genes affected

ZNF583 (HGNC:26427): (zinc finger protein 583) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585612.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF583	ENST00000585612.1	TSL:1	n.653+4400G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85751 AN: 151874 Hom.: 24585 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.565 AC: 85860 AN: 151992 Hom.: 24633 Cov.: 32 AF XY: 0.570 AC XY: 42313 AN XY: 74270

African (AFR) AF: 0.580 AC: 24040 AN: 41440

American (AMR) AF: 0.602 AC: 9207 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1486 AN: 3468

East Asian (EAS) AF: 0.879 AC: 4555 AN: 5184

South Asian (SAS) AF: 0.625 AC: 3012 AN: 4822

European-Finnish (FIN) AF: 0.608 AC: 6391 AN: 10512

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35295 AN: 67966

Other (OTH) AF: 0.536 AC: 1132 AN: 2112

Alfa AF: 0.507 Hom.: 9164

Bravo AF: 0.564

Asia WGS AF: 0.739 AC: 2566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.25
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs8104319; hg19: chr19-56939571;