dbSNP rs28559848: ZNF443:p.Ter672Leuext*? (chr19-12430157-T-A) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 2P and 8B. PM4BA1

The NM_005815.5(ZNF443):c.2015A>T(p.Ter672Leuext*?) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 1,610,318 control chromosomes in the GnomAD database, including 39,560 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 0.24 ( 4913 hom., cov: 32)

Exomes 𝑓: 0.21 ( 34647 hom. )

Consequence

ZNF443
NM_005815.5 stop_lost

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Publications

16 publications found

Variant links:

Genes affected

ZNF443 (HGNC:20878): (zinc finger protein 443) Zinc finger proteins (ZNFs) bind DNA and, through this binding, regulate gene transcription. Most ZNFs contain conserved C2H2 motifs and are classified as Kruppel-type zinc fingers. For a general description of these proteins, see ZNF91 (MIM 603971).[supplied by OMIM, Jul 2002]

ZNF443 links:

ENSG00000268870 (HGNC:):

ENSG00000268870 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

PM4

Stoplost variant in NM_005815.5 Downstream stopcodon found after 41 codons.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF443	NM_005815.5 link	c.2015A>T	p.Ter672Leuext*?	stop_lost	Exon 4 of 4	ENST00000301547.10	NP_005806.3	Q9Y2A4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF443	ENST00000301547.10 link	c.2015A>T	p.Ter672Leuext*?	stop_lost	Exon 4 of 4	1	NM_005815.5	ENSP00000301547.5		Q9Y2A4
ENSG00000268870	ENST00000595562.1 link	c.3+10755A>T		intron_variant	Intron 1 of 3	4		ENSP00000471613.1		M0R135

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

36730

AN:

151850

Hom.:

4899

Cov.:

show subpopulations

Gnomad AFR

AF:

0.358

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.365

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.322

Gnomad NFE

AF:

0.189

Gnomad OTH

AF:

0.258

GnomAD2 exomes

AF:

0.225

AC:

56081

AN:

249276

AF XY:

0.228

show subpopulations

Gnomad AFR exome

AF:

0.354

Gnomad AMR exome

AF:

0.285

Gnomad ASJ exome

AF:

0.258

Gnomad EAS exome

AF:

0.0999

Gnomad FIN exome

AF:

0.114

Gnomad NFE exome

AF:

0.191

Gnomad OTH exome

AF:

0.226

GnomAD4 exome

AF:

0.209

AC:

304584

AN:

1458350

Hom.:

34647

Cov.:

AF XY:

0.212

AC XY:

154131

AN XY:

725562

show subpopulations

African (AFR)

AF:

0.357

AC:

11734

AN:

32868

American (AMR)

AF:

0.281

AC:

12430

AN:

44216

Ashkenazi Jewish (ASJ)

AF:

0.267

AC:

6954

AN:

26052

East Asian (EAS)

AF:

0.128

AC:

5086

AN:

39678

South Asian (SAS)

AF:

0.369

AC:

31708

AN:

85922

European-Finnish (FIN)

AF:

0.121

AC:

6454

AN:

53380

Middle Eastern (MID)

AF:

0.329

AC:

1893

AN:

5748

European-Non Finnish (NFE)

AF:

0.194

AC:

215124

AN:

1110222

Other (OTH)

AF:

0.219

AC:

13201

AN:

60264

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.440

Heterozygous variant carriers

12195

24390

36585

48780

60975

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.242

AC:

36772

AN:

151968

Hom.:

4913

Cov.:

AF XY:

0.239

AC XY:

17728

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.358

AC:

14806

AN:

41388

American (AMR)

AF:

0.253

AC:

3862

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

889

AN:

3468

East Asian (EAS)

AF:

0.115

AC:

594

AN:

5166

South Asian (SAS)

AF:

0.365

AC:

1751

AN:

4794

European-Finnish (FIN)

AF:

0.114

AC:

1212

AN:

10586

Middle Eastern (MID)

AF:

0.312

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.189

AC:

12864

AN:

67958

Other (OTH)

AF:

0.265

AC:

560

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1329

2659

3988

5318

6647

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.210

Hom.:

1213

Bravo

AF:

0.257

ExAC

AF:

0.228

AC:

27647

Asia WGS

AF:

0.288

AC:

1004

AN:

3474

EpiCase

AF:

0.200

EpiControl

AF:

0.206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.5

(source)

DANN

Benign

0.58

Eigen

Benign

-0.16

Eigen_PC

Benign

-0.63

FATHMM_MKL

Benign

0.0043

PhyloP100

-1.6

Vest4

0.0

GERP RS

-1.3

Mutation Taster

=195/5

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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rs28559848

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