Genetic Variant ZNF600:c.-321G>A (chr19-52780882-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001321866.4(ZNF600):c.-321G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,104 control chromosomes in the GnomAD database, including 3,214 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 0.19 ( 3214 hom., cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ZNF600
NM_001321866.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

23 publications found

Variant links:

Genes affected

ZNF600 (HGNC:30951): (zinc finger protein 600) Predicted to enable DNA-binding transcription activator 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]

ZNF600 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=-1.04).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321866.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF600	NM_001321866.4	MANE Select	c.-321G>A	5_prime_UTR	Exon 3 of 6	NP_001308795.1	A0A3B3IT03
ZNF600	NM_001321867.3		c.-19-1975G>A	intron	N/A	NP_001308796.1	A0A3B3IT03
ZNF600	NM_198457.5		c.-99-1975G>A	intron	N/A	NP_940859.3	Q6ZNG1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF600	ENST00000692063.1	MANE Select	c.-321G>A	5_prime_UTR	Exon 3 of 6	ENSP00000509267.1	A0A3B3IT03
ZNF600	ENST00000338230.3	TSL:1	c.-99-1975G>A	intron	N/A	ENSP00000344791.2	Q6ZNG1
ZNF600	ENST00000688329.1		c.-214G>A	5_prime_UTR	Exon 2 of 6	ENSP00000509375.1	A0A3B3IT03

Frequencies

GnomAD3 genomes

AF:

0.192

AC:

29252

AN:

151984

Hom.:

3197

Cov.:

show subpopulations

Gnomad AFR

AF:

0.306

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.0957

Gnomad EAS

AF:

0.0562

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.171

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.193

AC:

29308

AN:

152104

Hom.:

3214

Cov.:

AF XY:

0.191

AC XY:

14185

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.306

AC:

12695

AN:

41472

American (AMR)

AF:

0.150

AC:

2299

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0957

AC:

332

AN:

3470

East Asian (EAS)

AF:

0.0561

AC:

291

AN:

5188

South Asian (SAS)

AF:

0.140

AC:

674

AN:

4822

European-Finnish (FIN)

AF:

0.173

AC:

1820

AN:

10548

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.158

AC:

10720

AN:

67994

Other (OTH)

AF:

0.171

AC:

361

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1202

2403

3605

4806

6008

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.169

Hom.:

5183

Bravo

AF:

0.195

Asia WGS

AF:

0.129

AC:

447

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

3.8

(source)

DANN

Benign

0.42

PhyloP100

-1.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over