dbSNP rs10420268: ZNF571-AS1:n.209+7018A>G (chr19-37556173-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 ENST00000585578.5(ZNF571-AS1):n.209+7018A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 697,602 control chromosomes in the GnomAD database, including 25,592 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 0.25 ( 5584 hom., cov: 32)

Exomes 𝑓: 0.24 ( 20008 hom. )

Consequence

ZNF571-AS1
ENST00000585578.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.131

Publications

4 publications found

Variant links:

Genes affected

ZNF571-AS1 (HGNC:44324): (ZNF571 antisense RNA 1)

ZNF571-AS1 links:

ZNF540 (HGNC:25331): (zinc finger protein 540) Enables translation repressor activity, mRNA regulatory element binding. Involved in negative regulation of transcription, DNA-templated and negative regulation of translation. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF540 links:

ZNF571 (HGNC:25000): (zinc finger protein 571) 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. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF571 links:

Genome browser will be placed here

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=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
ZNF540	NM_152606.5 link	c.-73+4508A>G	intron_variant	Intron 1 of 4	NP_689819.1	Q8NDQ6-1
ZNF571-AS1	NR_038247.1 link	n.207+7018A>G	intron_variant	Intron 1 of 4
ZNF571-AS1	NR_038248.1 link	n.337+5182A>G	intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ZNF571-AS1	ENST00000585578.5 link	n.209+7018A>G	intron_variant	Intron 1 of 4	1
ZNF571-AS1	ENST00000586013.5 link	n.294+4508A>G	intron_variant	Intron 1 of 2	1
ZNF571-AS1	ENST00000586139.5 link	n.335+5182A>G	intron_variant	Intron 2 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

38529

AN:

151900

Hom.:

5577

Cov.:

show subpopulations

Gnomad AFR

AF:

0.327

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.242

Gnomad EAS

AF:

0.636

Gnomad SAS

AF:

0.339

Gnomad FIN

AF:

0.220

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.177

Gnomad OTH

AF:

0.248

GnomAD2 exomes

AF:

0.269

AC:

35464

AN:

131692

AF XY:

0.267

show subpopulations

Gnomad AFR exome

AF:

0.335

Gnomad AMR exome

AF:

0.289

Gnomad ASJ exome

AF:

0.222

Gnomad EAS exome

AF:

0.634

Gnomad FIN exome

AF:

0.225

Gnomad NFE exome

AF:

0.178

Gnomad OTH exome

AF:

0.216

GnomAD4 exome

AF:

0.240

AC:

130884

AN:

545584

Hom.:

20008

Cov.:

AF XY:

0.240

AC XY:

70806

AN XY:

294916

show subpopulations

African (AFR)

AF:

0.331

AC:

5190

AN:

15662

American (AMR)

AF:

0.284

AC:

9773

AN:

34442

Ashkenazi Jewish (ASJ)

AF:

0.223

AC:

4424

AN:

19798

East Asian (EAS)

AF:

0.668

AC:

21416

AN:

32070

South Asian (SAS)

AF:

0.304

AC:

18908

AN:

62244

European-Finnish (FIN)

AF:

0.217

AC:

7261

AN:

33452

Middle Eastern (MID)

AF:

0.229

AC:

894

AN:

3908

European-Non Finnish (NFE)

AF:

0.179

AC:

56275

AN:

313704

Other (OTH)

AF:

0.223

AC:

6743

AN:

30304

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

4838

9675

14513

19350

24188

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

502

1004

1506

2008

2510

<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:

0.254

AC:

38554

AN:

152018

Hom.:

5584

Cov.:

AF XY:

0.258

AC XY:

19169

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.327

AC:

13552

AN:

41430

American (AMR)

AF:

0.269

AC:

4116

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.242

AC:

840

AN:

3472

East Asian (EAS)

AF:

0.636

AC:

3277

AN:

5154

South Asian (SAS)

AF:

0.338

AC:

1622

AN:

4804

European-Finnish (FIN)

AF:

0.220

AC:

2332

AN:

10586

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.177

AC:

12047

AN:

67976

Other (OTH)

AF:

0.245

AC:

516

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1392

2784

4175

5567

6959

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.213

Hom.:

735

Bravo

AF:

0.259

Asia WGS

AF:

0.433

AC:

1504

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

(source)

DANN

Benign

0.89

PhyloP100

0.13

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over