rs8104319

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr19-56428202-G-A
• chr19-56428202-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

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
ZNF583	ENST00000585612.1	n.653+4400G>A		intron_variant	Intron 1 of 1	1

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

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.536

Alfa AF: 0.505 Hom.: 8019

Bravo AF: 0.564

Asia WGS AF: 0.739 AC: 2566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8104319; hg19: chr19-56939571;