Genetic Variant ZNF318:c.3496-123G>A (chr6-43340625-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_014345.3(ZNF318):c.3496-123G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 1,503,926 control chromosomes in the GnomAD database, including 82,663 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 0.41 ( 15072 hom., cov: 32)

Exomes 𝑓: 0.31 ( 67591 hom. )

Consequence

ZNF318
NM_014345.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.96

Publications

37 publications found

Variant links:

Genes affected

ZNF318 (HGNC:13578): (zinc finger protein 318) Predicted to enable protein heterodimerization activity and protein homodimerization activity. Predicted to be involved in negative regulation of transcription, DNA-templated and positive regulation of transcription, DNA-templated. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF318 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014345.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF318	NM_014345.3	MANE Select	c.3496-123G>A		intron	N/A	NP_055160.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF318	ENST00000361428.3	TSL:1 MANE Select	c.3496-123G>A	intron	N/A	ENSP00000354964.2
ZNF318	ENST00000605935.5	TSL:1	n.3276+2051G>A	intron	N/A	ENSP00000475748.1
ZNF318	ENST00000606599.1	TSL:2	c.159+2051G>A	intron	N/A	ENSP00000475511.1

Frequencies

GnomAD3 genomes

AF:

0.413

AC:

62832

AN:

151992

Hom.:

15045

Cov.:

show subpopulations

Gnomad AFR

AF:

0.669

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.381

Gnomad ASJ

AF:

0.372

Gnomad EAS

AF:

0.333

Gnomad SAS

AF:

0.402

Gnomad FIN

AF:

0.267

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.299

Gnomad OTH

AF:

0.422

GnomAD4 exome

AF:

0.308

AC:

416677

AN:

1351816

Hom.:

67591

Cov.:

AF XY:

0.310

AC XY:

206019

AN XY:

664262

show subpopulations

African (AFR)

AF:

0.690

AC:

20305

AN:

29436

American (AMR)

AF:

0.402

AC:

10828

AN:

26918

Ashkenazi Jewish (ASJ)

AF:

0.355

AC:

7203

AN:

20304

East Asian (EAS)

AF:

0.328

AC:

12276

AN:

37406

South Asian (SAS)

AF:

0.387

AC:

26268

AN:

67812

European-Finnish (FIN)

AF:

0.276

AC:

12468

AN:

45130

Middle Eastern (MID)

AF:

0.471

AC:

2420

AN:

5134

European-Non Finnish (NFE)

AF:

0.287

AC:

305775

AN:

1063798

Other (OTH)

AF:

0.342

AC:

19134

AN:

55878

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

15005

30010

45014

60019

75024

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10506

21012

31518

42024

52530

<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:

0.414

AC:

62915

AN:

152110

Hom.:

15072

Cov.:

AF XY:

0.410

AC XY:

30521

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.669

AC:

27747

AN:

41490

American (AMR)

AF:

0.382

AC:

5838

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.372

AC:

1293

AN:

3472

East Asian (EAS)

AF:

0.334

AC:

1733

AN:

5186

South Asian (SAS)

AF:

0.403

AC:

1943

AN:

4826

European-Finnish (FIN)

AF:

0.267

AC:

2817

AN:

10554

Middle Eastern (MID)

AF:

0.425

AC:

124

AN:

292

European-Non Finnish (NFE)

AF:

0.299

AC:

20358

AN:

67980

Other (OTH)

AF:

0.421

AC:

887

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1728

3456

5183

6911

8639

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

556

1112

1668

2224

2780

<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:

0.354

Hom.:

2629

Bravo

AF:

0.432

Asia WGS

AF:

0.380

AC:

1321

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.047

(source)

DANN

Benign

0.50

PhyloP100

-2.0

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