dbSNP rs10853854: 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:

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=-0.99).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
ZNF611	NM_001161499.2 link	c.-121-44C>T	intron_variant	Intron 2 of 5	ENST00000652185.1	NP_001154971.1
ZNF611	NM_001161500.2 link	c.-121-44C>T	intron_variant	Intron 1 of 4		NP_001154972.1
ZNF611	NM_030972.3 link	c.-244-44C>T	intron_variant	Intron 2 of 6		NP_112234.3
ZNF611	NM_001161501.1 link	c.-201-44C>T	intron_variant	Intron 2 of 4		NP_001154973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF611	ENST00000652185.1 link	c.-121-44C>T		intron_variant	Intron 2 of 5		NM_001161499.2	ENSP00000498713.1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over