Genetic Variant ZNF618:c.551-115C>T (chr9-114007235-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_001318042.2(ZNF618):c.551-115C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 801,416 control chromosomes in the GnomAD database, including 159,434 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 0.55 ( 24938 hom., cov: 31)

Exomes 𝑓: 0.64 ( 134496 hom. )

Consequence

ZNF618
NM_001318042.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.27

Publications

5 publications found

Variant links:

Genes affected

ZNF618 (HGNC:29416): (zinc finger protein 618) Enables identical protein binding activity and transcription coregulator binding activity. Involved in positive regulation of chromatin binding activity. Located in chromatin. Part of pericentric heterochromatin. [provided by Alliance of Genome Resources, Apr 2022]

ZNF618 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318042.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF618	NM_001318042.2	MANE Select	c.551-115C>T	intron	N/A	NP_001304971.1	Q5T7W0-1
ZNF618	NM_001318041.2		c.455-115C>T	intron	N/A	NP_001304970.1
ZNF618	NM_001318040.2		c.455-115C>T	intron	N/A	NP_001304969.1	Q5T7W0-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF618	ENST00000374126.10	TSL:1 MANE Select	c.551-115C>T	intron	N/A	ENSP00000363241.5	Q5T7W0-1
ZNF618	ENST00000615615.4	TSL:1	c.455-115C>T	intron	N/A	ENSP00000483198.1	Q5T7W0-4
ZNF618	ENST00000968409.1		c.551-115C>T	intron	N/A	ENSP00000638468.1

Frequencies

GnomAD3 genomes

AF:

0.549

AC:

83337

AN:

151878

Hom.:

24936

Cov.:

show subpopulations

Gnomad AFR

AF:

0.293

Gnomad AMI

AF:

0.792

Gnomad AMR

AF:

0.542

Gnomad ASJ

AF:

0.636

Gnomad EAS

AF:

0.628

Gnomad SAS

AF:

0.624

Gnomad FIN

AF:

0.715

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.661

Gnomad OTH

AF:

0.535

GnomAD4 exome

AF:

0.639

AC:

415050

AN:

649420

Hom.:

134496

AF XY:

0.640

AC XY:

215847

AN XY:

337356

show subpopulations

African (AFR)

AF:

0.281

AC:

4577

AN:

16316

American (AMR)

AF:

0.556

AC:

14287

AN:

25678

Ashkenazi Jewish (ASJ)

AF:

0.644

AC:

10551

AN:

16380

East Asian (EAS)

AF:

0.674

AC:

21316

AN:

31606

South Asian (SAS)

AF:

0.620

AC:

32474

AN:

52338

European-Finnish (FIN)

AF:

0.713

AC:

27574

AN:

38696

Middle Eastern (MID)

AF:

0.512

AC:

2054

AN:

4010

European-Non Finnish (NFE)

AF:

0.654

AC:

282303

AN:

431456

Other (OTH)

AF:

0.605

AC:

19914

AN:

32940

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

7201

14401

21602

28802

36003

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4242

8484

12726

16968

21210

<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:

0.548

AC:

83357

AN:

151996

Hom.:

24938

Cov.:

AF XY:

0.551

AC XY:

40966

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.293

AC:

12143

AN:

41448

American (AMR)

AF:

0.541

AC:

8273

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.636

AC:

2204

AN:

3466

East Asian (EAS)

AF:

0.627

AC:

3226

AN:

5144

South Asian (SAS)

AF:

0.625

AC:

3004

AN:

4808

European-Finnish (FIN)

AF:

0.715

AC:

7563

AN:

10582

Middle Eastern (MID)

AF:

0.575

AC:

169

AN:

294

European-Non Finnish (NFE)

AF:

0.661

AC:

44932

AN:

67946

Other (OTH)

AF:

0.531

AC:

1121

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1727

3455

5182

6910

8637

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

716

1432

2148

2864

3580

<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:

0.633

Hom.:

15806

Bravo

AF:

0.522

Asia WGS

AF:

0.567

AC:

1975

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.36

(source)

DANN

Benign

0.86

PhyloP100

-2.3

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