Genetic Variant ZNF627:c.*98A>G (chr19-11617987-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_145295.4(ZNF627):c.*98A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,042,496 control chromosomes in the GnomAD database, including 35,232 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 ( 4468 hom., cov: 32)

Exomes 𝑓: 0.26 ( 30764 hom. )

Consequence

ZNF627
NM_145295.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.810

Publications

18 publications found

Variant links:

Genes affected

ZNF627 (HGNC:30570): (zinc finger protein 627) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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]

ZNF627 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=-0.65).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145295.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF627	NM_145295.4	MANE Select	c.*98A>G	3_prime_UTR	Exon 4 of 4	NP_660338.1
ZNF627	NM_001290083.2		c.*98A>G	3_prime_UTR	Exon 5 of 5	NP_001277012.1
ZNF627	NM_001290084.3		c.*98A>G	3_prime_UTR	Exon 4 of 4	NP_001277013.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF627	ENST00000361113.10	TSL:1 MANE Select	c.*98A>G		3_prime_UTR	Exon 4 of 4	ENSP00000354414.4
	ZNF627	ENST00000588174.1	TSL:2	c.*1269A>G		3_prime_UTR	Exon 4 of 4	ENSP00000465841.1

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36423

AN:

152034

Hom.:

4468

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.298

Gnomad ASJ

AF:

0.369

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.239

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.274

GnomAD4 exome

AF:

0.262

AC:

233095

AN:

890346

Hom.:

30764

Cov.:

AF XY:

0.262

AC XY:

117401

AN XY:

448010

show subpopulations

African (AFR)

AF:

0.177

AC:

3638

AN:

20522

American (AMR)

AF:

0.303

AC:

6328

AN:

20876

Ashkenazi Jewish (ASJ)

AF:

0.363

AC:

5977

AN:

16472

East Asian (EAS)

AF:

0.128

AC:

4344

AN:

33816

South Asian (SAS)

AF:

0.240

AC:

12269

AN:

51102

European-Finnish (FIN)

AF:

0.231

AC:

7376

AN:

31870

Middle Eastern (MID)

AF:

0.310

AC:

1368

AN:

4416

European-Non Finnish (NFE)

AF:

0.270

AC:

181219

AN:

670930

Other (OTH)

AF:

0.262

AC:

10576

AN:

40342

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

8620

17241

25861

34482

43102

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5338

10676

16014

21352

26690

<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:

0.239

AC:

36435

AN:

152150

Hom.:

4468

Cov.:

AF XY:

0.242

AC XY:

17977

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.176

AC:

7306

AN:

41512

American (AMR)

AF:

0.298

AC:

4548

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.369

AC:

1281

AN:

3472

East Asian (EAS)

AF:

0.139

AC:

720

AN:

5176

South Asian (SAS)

AF:

0.238

AC:

1149

AN:

4830

European-Finnish (FIN)

AF:

0.239

AC:

2525

AN:

10586

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.265

AC:

17999

AN:

67990

Other (OTH)

AF:

0.273

AC:

577

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1419

2838

4258

5677

7096

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

388

776

1164

1552

1940

<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:

0.246

Hom.:

4258

Bravo

AF:

0.241

Asia WGS

AF:

0.197

AC:

683

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

3.9

(source)

DANN

Benign

0.68

PhyloP100

0.81

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