dbSNP rs12737: ZNF597:c.*139G>T (chr16-3436285-C-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_152457.3(ZNF597):c.*139G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 825,182 control chromosomes in the GnomAD database, including 285,916 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 0.80 ( 48775 hom., cov: 33)

Exomes 𝑓: 0.84 ( 237141 hom. )

Consequence

ZNF597
NM_152457.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0420

Publications

15 publications found

Variant links:

Genes affected

ZNF597 (HGNC:26573): (zinc finger protein 597) This gene encodes a protein with multiple zinc finger domains. Loss of the related gene in rodents results in defects in neural development and embryonic lethality in mutant homozygotes. This gene is adjacent to a differentially methylated region (DMR) and is imprinted and maternally expressed. [provided by RefSeq, Nov 2015]

ZNF597 links:

ENSG00000285329 (HGNC:):

ENSG00000285329 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152457.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF597	NM_152457.3	MANE Select	c.*139G>T		3_prime_UTR	Exon 4 of 4	NP_689670.1	Q96LX8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF597	ENST00000301744.7	TSL:1 MANE Select	c.*139G>T		3_prime_UTR	Exon 4 of 4	ENSP00000301744.4	Q96LX8
	ENSG00000285329	ENST00000575785.2	TSL:4	n.212-12186C>A		intron	N/A	ENSP00000477472.1	V9GZ69

Frequencies

GnomAD3 genomes

AF:

0.798

AC:

121287

AN:

152066

Hom.:

48744

Cov.:

show subpopulations

Gnomad AFR

AF:

0.686

Gnomad AMI

AF:

0.826

Gnomad AMR

AF:

0.863

Gnomad ASJ

AF:

0.796

Gnomad EAS

AF:

0.818

Gnomad SAS

AF:

0.833

Gnomad FIN

AF:

0.822

Gnomad MID

AF:

0.685

Gnomad NFE

AF:

0.843

Gnomad OTH

AF:

0.785

GnomAD4 exome

AF:

0.838

AC:

564237

AN:

672998

Hom.:

237141

Cov.:

AF XY:

0.839

AC XY:

287452

AN XY:

342768

show subpopulations

African (AFR)

AF:

0.681

AC:

11350

AN:

16662

American (AMR)

AF:

0.882

AC:

16361

AN:

18554

Ashkenazi Jewish (ASJ)

AF:

0.781

AC:

11802

AN:

15116

East Asian (EAS)

AF:

0.845

AC:

27161

AN:

32140

South Asian (SAS)

AF:

0.840

AC:

41171

AN:

48996

European-Finnish (FIN)

AF:

0.831

AC:

26046

AN:

31352

Middle Eastern (MID)

AF:

0.755

AC:

1819

AN:

2410

European-Non Finnish (NFE)

AF:

0.846

AC:

401199

AN:

474422

Other (OTH)

AF:

0.820

AC:

27328

AN:

33346

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

4596

9191

13787

18382

22978

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6118

12236

18354

24472

30590

<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:

0.798

AC:

121373

AN:

152184

Hom.:

48775

Cov.:

AF XY:

0.798

AC XY:

59375

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.686

AC:

28475

AN:

41492

American (AMR)

AF:

0.863

AC:

13199

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.796

AC:

2765

AN:

3472

East Asian (EAS)

AF:

0.818

AC:

4237

AN:

5180

South Asian (SAS)

AF:

0.832

AC:

4019

AN:

4828

European-Finnish (FIN)

AF:

0.822

AC:

8706

AN:

10588

Middle Eastern (MID)

AF:

0.678

AC:

198

AN:

292

European-Non Finnish (NFE)

AF:

0.843

AC:

57365

AN:

68024

Other (OTH)

AF:

0.785

AC:

1657

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1260

2520

3780

5040

6300

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

876

1752

2628

3504

4380

<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:

0.826

Hom.:

69779

Bravo

AF:

0.797

Asia WGS

AF:

0.838

AC:

2914

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.3

(source)

DANN

Benign

0.51

PhyloP100

0.042

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