Genetic Variant ZNF611:c.-121-44C>T (chr19-52728875-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001161499.2(ZNF611):c.-121-44C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 166,670 control chromosomes in the GnomAD database, including 11,073 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 0.37 ( 10543 hom., cov: 32)

Exomes 𝑓: 0.27 ( 530 hom. )

Consequence

ZNF611
NM_001161499.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0850

Publications

7 publications found

Variant links:

Genes affected

ZNF611 (HGNC:28766): (zinc finger protein 611) 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]

ZNF611 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001161499.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF611	NM_001161499.2	MANE Select	c.-121-44C>T	intron	N/A	NP_001154971.1
ZNF611	NM_001161500.2		c.-121-44C>T	intron	N/A	NP_001154972.1
ZNF611	NM_030972.3		c.-244-44C>T	intron	N/A	NP_112234.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF611	ENST00000652185.1	MANE Select	c.-121-44C>T	intron	N/A	ENSP00000498713.1
ZNF611	ENST00000595001.5	TSL:1	n.-244-44C>T	intron	N/A	ENSP00000471243.1
ZNF611	ENST00000319783.5	TSL:2	c.-244-44C>T	intron	N/A	ENSP00000322427.1

Frequencies

GnomAD3 genomes

AF:

0.366

AC:

55506

AN:

151846

Hom.:

10529

Cov.:

show subpopulations

Gnomad AFR

AF:

0.465

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.328

Gnomad ASJ

AF:

0.421

Gnomad EAS

AF:

0.433

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.301

Gnomad MID

AF:

0.296

Gnomad NFE

AF:

0.322

Gnomad OTH

AF:

0.355

GnomAD4 exome

AF:

0.269

AC:

3955

AN:

14706

Hom.:

530

Cov.:

AF XY:

0.267

AC XY:

2389

AN XY:

8962

show subpopulations

African (AFR)

AF:

0.410

AC:

110

AN:

268

American (AMR)

AF:

0.266

AC:

401

AN:

1510

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

AN:

202

East Asian (EAS)

AF:

0.382

AC:

331

AN:

866

South Asian (SAS)

AF:

0.216

AC:

271

AN:

1254

European-Finnish (FIN)

AF:

0.262

AC:

932

AN:

3560

Middle Eastern (MID)

AF:

0.233

AC:

AN:

European-Non Finnish (NFE)

AF:

0.261

AC:

1693

AN:

6492

Other (OTH)

AF:

0.277

AC:

145

AN:

524

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

136

272

409

545

681

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

136

170

<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:

0.366

AC:

55566

AN:

151964

Hom.:

10543

Cov.:

AF XY:

0.366

AC XY:

27202

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.465

AC:

19280

AN:

41448

American (AMR)

AF:

0.327

AC:

4999

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.421

AC:

1460

AN:

3470

East Asian (EAS)

AF:

0.433

AC:

2227

AN:

5138

South Asian (SAS)

AF:

0.275

AC:

1323

AN:

4814

European-Finnish (FIN)

AF:

0.301

AC:

3182

AN:

10568

Middle Eastern (MID)

AF:

0.308

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.322

AC:

21913

AN:

67954

Other (OTH)

AF:

0.350

AC:

737

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1789

3578

5368

7157

8946

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

536

1072

1608

2144

2680

<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:

0.347

Hom.:

3223

Bravo

AF:

0.372

Asia WGS

AF:

0.366

AC:

1271

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

3.2

(source)

DANN

Benign

0.27

PhyloP100

-0.085

PromoterAI

0.033

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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