dbSNP rs917652: ZNF583:c.233-149A>G (chr19-56422742-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.57 ( 24850 hom., cov: 32)

Exomes 𝑓: 0.56 ( 61751 hom. )

Consequence

ZNF583
NM_152478.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.83

Publications

6 publications found

Variant links:

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]

ZNF583 links:

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ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF583	NM_152478.3	MANE Select	c.233-149A>G	intron	N/A	NP_689691.2	Q96ND8
ZNF583	NM_001159860.2		c.233-149A>G	intron	N/A	NP_001153332.1	Q96ND8
ZNF583	NM_001159861.2		c.233-149A>G	intron	N/A	NP_001153333.1	Q96ND8

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF583	ENST00000333201.13	TSL:2 MANE Select	c.233-149A>G	intron	N/A	ENSP00000388502.2	Q96ND8
ZNF583	ENST00000890730.1		c.236-149A>G	intron	N/A	ENSP00000560789.1
ZNF583	ENST00000969490.1		c.236-149A>G	intron	N/A	ENSP00000639549.1

Frequencies

GnomAD3 genomes

AF:

0.567

AC:

86110

AN:

151862

Hom.:

24801

Cov.:

show subpopulations

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

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

4160

8319

12479

16638

20798

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1294

2588

3882

5176

6470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.567

AC:

86217

AN:

151980

Hom.:

24850

Cov.:

AF XY:

0.572

AC XY:

42494

AN XY:

74286

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1841

3682

5523

7364

9205

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

740

1480

2220

2960

3700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.68

PhyloP100

-2.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over