NM_152478.3:c.233-149A>G

Variant names:

• chr19-56422742-A-G
• rs917652
• NM_152478.3:c.233-149A>G

Variant summary

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

The NM_152478.3(ZNF583):​c.233-149A>G 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 525,936 control chromosomes in the GnomAD database, including 86,601 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 0.57 (24850 hom., cov: 32)
  • Exomes 𝑓: 0.56 (61751 hom.)
• Consequence: ZNF583 NM_152478.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152478.3. 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
	ZNF583	NM_152478.3	MANE Select	c.233-149A>G		intron	N/A	NP_689691.2
	ZNF583	NM_001159860.2		c.233-149A>G		intron	N/A	NP_001153332.1
	ZNF583	NM_001159861.2		c.233-149A>G		intron	N/A	NP_001153333.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF583	ENST00000333201.13	TSL:2 MANE Select	c.233-149A>G		intron	N/A	ENSP00000388502.2
	ZNF583	ENST00000291598.11	TSL:3	c.233-149A>G		intron	N/A	ENSP00000291598.7
	ZNF583	ENST00000391778.3	TSL:4	c.233-149A>G		intron	N/A	ENSP00000375657.3

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86110 AN: 151862 Hom.: 24801 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.536

GnomAD4 exome AF: 0.564 AC: 211005 AN: 373956 Hom.: 61751 AF XY: 0.565 AC XY: 109499 AN XY: 193970

African (AFR) AF: 0.597 AC: 5339 AN: 8944

American (AMR) AF: 0.625 AC: 6850 AN: 10966

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 4956 AN: 11092

East Asian (EAS) AF: 0.882 AC: 22258 AN: 25222

South Asian (SAS) AF: 0.619 AC: 15075 AN: 24358

European-Finnish (FIN) AF: 0.623 AC: 14815 AN: 23762

Middle Eastern (MID) AF: 0.458 AC: 737 AN: 1608

European-Non Finnish (NFE) AF: 0.524 AC: 129024 AN: 246396

Other (OTH) AF: 0.553 AC: 11951 AN: 21608

GnomAD4 genome AF: 0.567 AC: 86217 AN: 151980 Hom.: 24850 Cov.: 32 AF XY: 0.572 AC XY: 42494 AN XY: 74286

African (AFR) AF: 0.587 AC: 24319 AN: 41434

American (AMR) AF: 0.606 AC: 9258 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1484 AN: 3466

East Asian (EAS) AF: 0.879 AC: 4562 AN: 5188

South Asian (SAS) AF: 0.624 AC: 3008 AN: 4818

European-Finnish (FIN) AF: 0.609 AC: 6430 AN: 10554

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35277 AN: 67928

Other (OTH) AF: 0.539 AC: 1136 AN: 2108

Alfa AF: 0.548 Hom.: 3178

Bravo AF: 0.567

Asia WGS AF: 0.739 AC: 2551 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.065
DANN	Benign	0.68
PhyloP100		-2.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs917652; hg19: chr19-56934111;