dbSNP rs4986773: ZNF350:p.Asp35Asp (chr19-51969042-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_021632.4(ZNF350):c.105T>C(p.Asp35Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 1,613,682 control chromosomes in the GnomAD database, including 81,057 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 0.39 ( 13331 hom., cov: 31)

Exomes 𝑓: 0.29 ( 67726 hom. )

Consequence

ZNF350
NM_021632.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -6.05

Publications

18 publications found

Variant links:

Genes affected

ZNF350 (HGNC:16656): (zinc finger protein 350) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nuclear body. Part of transcription repressor complex. [provided by Alliance of Genome Resources, Apr 2022]

ZNF350 links:

ZNF350-AS1 (HGNC:48598): (ZNF350 antisense RNA 1)

ZNF350-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BP7

Synonymous conserved (PhyloP=-6.05 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF350	NM_021632.4 link	c.105T>C	p.Asp35Asp	synonymous_variant	Exon 3 of 5	ENST00000243644.9	NP_067645.3	Q9GZX5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF350	ENST00000243644.9 link	c.105T>C	p.Asp35Asp	synonymous_variant	Exon 3 of 5	1	NM_021632.4	ENSP00000243644.3		Q9GZX5

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58548

AN:

151852

Hom.:

13279

Cov.:

show subpopulations

Gnomad AFR

AF:

0.631

Gnomad AMI

AF:

0.356

Gnomad AMR

AF:

0.294

Gnomad ASJ

AF:

0.303

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.546

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.371

GnomAD2 exomes

AF:

0.332

AC:

83424

AN:

251450

AF XY:

0.335

show subpopulations

Gnomad AFR exome

AF:

0.639

Gnomad AMR exome

AF:

0.256

Gnomad ASJ exome

AF:

0.307

Gnomad EAS exome

AF:

0.285

Gnomad FIN exome

AF:

0.334

Gnomad NFE exome

AF:

0.267

Gnomad OTH exome

AF:

0.306

GnomAD4 exome

AF:

0.291

AC:

425528

AN:

1461710

Hom.:

67726

Cov.:

AF XY:

0.297

AC XY:

215865

AN XY:

727152

show subpopulations

African (AFR)

AF:

0.643

AC:

21528

AN:

33478

American (AMR)

AF:

0.264

AC:

11808

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.303

AC:

7928

AN:

26128

East Asian (EAS)

AF:

0.290

AC:

11493

AN:

39688

South Asian (SAS)

AF:

0.520

AC:

44886

AN:

86256

European-Finnish (FIN)

AF:

0.326

AC:

17409

AN:

53412

Middle Eastern (MID)

AF:

0.297

AC:

1712

AN:

5768

European-Non Finnish (NFE)

AF:

0.261

AC:

289844

AN:

1111884

Other (OTH)

AF:

0.313

AC:

18920

AN:

60378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

17184

34368

51552

68736

85920

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10074

20148

30222

40296

50370

<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:

0.386

AC:

58662

AN:

151972

Hom.:

13331

Cov.:

AF XY:

0.391

AC XY:

29005

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.632

AC:

26162

AN:

41410

American (AMR)

AF:

0.294

AC:

4485

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.303

AC:

1051

AN:

3468

East Asian (EAS)

AF:

0.286

AC:

1473

AN:

5156

South Asian (SAS)

AF:

0.546

AC:

2630

AN:

4818

European-Finnish (FIN)

AF:

0.343

AC:

3623

AN:

10554

Middle Eastern (MID)

AF:

0.306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.265

AC:

18028

AN:

67966

Other (OTH)

AF:

0.376

AC:

796

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1627

3254

4880

6507

8134

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

550

1100

1650

2200

2750

<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:

0.321

Hom.:

4044

Bravo

AF:

0.388

Asia WGS

AF:

0.494

AC:

1719

AN:

3478

EpiCase

AF:

0.268

EpiControl

AF:

0.268

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.19

(source)

DANN

Benign

0.26

PhyloP100

-6.0

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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