dbSNP rs2075852: ZNF200:c.340-58A>G (chr16-3232605-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_198088.3(ZNF200):c.340-58A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 1,596,994 control chromosomes in the GnomAD database, including 183,865 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.44 ( 14939 hom., cov: 32)

Exomes 𝑓: 0.48 ( 168926 hom. )

Consequence

ZNF200
NM_198088.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00400

Publications

16 publications found

Variant links:

Genes affected

ZNF200 (HGNC:12993): (zinc finger protein 200) Predicted to enable metal ion binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF200 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198088.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF200	NM_198088.3	MANE Select	c.340-58A>G	intron	N/A	NP_932354.1	P98182-1
ZNF200	NM_003454.4		c.340-58A>G	intron	N/A	NP_003445.2
ZNF200	NM_001145446.2		c.340-58A>G	intron	N/A	NP_001138918.1	P98182-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF200	ENST00000414144.7	TSL:1 MANE Select	c.340-58A>G	intron	N/A	ENSP00000405786.2	P98182-1
ZNF200	ENST00000431561.7	TSL:1	c.340-58A>G	intron	N/A	ENSP00000395723.3	P98182-1
ZNF200	ENST00000396868.7	TSL:1	c.340-61A>G	intron	N/A	ENSP00000380077.3	P98182-2

Frequencies

GnomAD3 genomes

AF:

0.435

AC:

66080

AN:

151816

Hom.:

14923

Cov.:

show subpopulations

Gnomad AFR

AF:

0.302

Gnomad AMI

AF:

0.418

Gnomad AMR

AF:

0.533

Gnomad ASJ

AF:

0.446

Gnomad EAS

AF:

0.582

Gnomad SAS

AF:

0.418

Gnomad FIN

AF:

0.483

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.477

Gnomad OTH

AF:

0.436

GnomAD4 exome

AF:

0.480

AC:

694247

AN:

1445060

Hom.:

168926

Cov.:

AF XY:

0.478

AC XY:

343313

AN XY:

718812

show subpopulations

African (AFR)

AF:

0.292

AC:

9559

AN:

32784

American (AMR)

AF:

0.645

AC:

27701

AN:

42946

Ashkenazi Jewish (ASJ)

AF:

0.441

AC:

11101

AN:

25192

East Asian (EAS)

AF:

0.582

AC:

23057

AN:

39636

South Asian (SAS)

AF:

0.422

AC:

35491

AN:

84062

European-Finnish (FIN)

AF:

0.489

AC:

23705

AN:

48452

Middle Eastern (MID)

AF:

0.430

AC:

2437

AN:

5672

European-Non Finnish (NFE)

AF:

0.482

AC:

533223

AN:

1106532

Other (OTH)

AF:

0.468

AC:

27973

AN:

59784

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

18912

37825

56737

75650

94562

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15738

31476

47214

62952

78690

<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:

0.435

AC:

66130

AN:

151934

Hom.:

14939

Cov.:

AF XY:

0.438

AC XY:

32538

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.303

AC:

12540

AN:

41444

American (AMR)

AF:

0.534

AC:

8151

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.446

AC:

1547

AN:

3466

East Asian (EAS)

AF:

0.582

AC:

2994

AN:

5144

South Asian (SAS)

AF:

0.417

AC:

2009

AN:

4816

European-Finnish (FIN)

AF:

0.483

AC:

5080

AN:

10526

Middle Eastern (MID)

AF:

0.388

AC:

114

AN:

294

European-Non Finnish (NFE)

AF:

0.477

AC:

32398

AN:

67958

Other (OTH)

AF:

0.435

AC:

916

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1931

3862

5792

7723

9654

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

626

1252

1878

2504

3130

<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:

0.462

Hom.:

21479

Bravo

AF:

0.440

Asia WGS

AF:

0.482

AC:

1673

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.2

(source)

DANN

Benign

0.49

PhyloP100

0.0040

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