Genetic Variant ZNF350:c.238+18A>G (chr19-51968560-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_021632.4(ZNF350):c.238+18A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 1,608,078 control chromosomes in the GnomAD database, including 80,835 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 0.39 ( 13334 hom., cov: 31)

Exomes 𝑓: 0.29 ( 67501 hom. )

Consequence

ZNF350
NM_021632.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.756

Publications

11 publications found

Variant links:

Genes affected

ZNF350 (HGNC:16656): (zinc finger protein 350) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nuclear body. Part of transcription repressor complex. [provided by Alliance of Genome Resources, Apr 2022]

ZNF350 links:

ZNF350-AS1 (HGNC:48598): (ZNF350 antisense RNA 1)

ZNF350-AS1 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021632.4. 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
	ZNF350	NM_021632.4	MANE Select	c.238+18A>G		intron	N/A	NP_067645.3
	ZNF350-AS1	NR_103847.1		n.103-7831T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF350	ENST00000243644.9	TSL:1 MANE Select	c.238+18A>G	intron	N/A	ENSP00000243644.3	Q9GZX5
ZNF350-AS1	ENST00000595010.5	TSL:1	n.125-7831T>C	intron	N/A
ZNF350	ENST00000853589.1		c.238+18A>G	intron	N/A	ENSP00000523648.1

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58536

AN:

151774

Hom.:

13282

Cov.:

show subpopulations

Gnomad AFR

AF:

0.631

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.295

Gnomad ASJ

AF:

0.303

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.548

Gnomad FIN

AF:

0.344

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.370

GnomAD2 exomes

AF:

0.332

AC:

83378

AN:

251244

AF XY:

0.335

show subpopulations

Gnomad AFR exome

AF:

0.639

Gnomad AMR exome

AF:

0.256

Gnomad ASJ exome

AF:

0.307

Gnomad EAS exome

AF:

0.286

Gnomad FIN exome

AF:

0.334

Gnomad NFE exome

AF:

0.267

Gnomad OTH exome

AF:

0.306

GnomAD4 exome

AF:

0.291

AC:

423535

AN:

1456184

Hom.:

67501

Cov.:

AF XY:

0.297

AC XY:

214959

AN XY:

724706

show subpopulations

African (AFR)

AF:

0.643

AC:

21444

AN:

33344

American (AMR)

AF:

0.264

AC:

11802

AN:

44700

Ashkenazi Jewish (ASJ)

AF:

0.303

AC:

7915

AN:

26090

East Asian (EAS)

AF:

0.289

AC:

11481

AN:

39662

South Asian (SAS)

AF:

0.520

AC:

44804

AN:

86132

European-Finnish (FIN)

AF:

0.326

AC:

17396

AN:

53388

Middle Eastern (MID)

AF:

0.296

AC:

1704

AN:

5748

European-Non Finnish (NFE)

AF:

0.260

AC:

288137

AN:

1106896

Other (OTH)

AF:

0.313

AC:

18852

AN:

60224

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

13287

26574

39860

53147

66434

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9990

19980

29970

39960

49950

<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:

0.386

AC:

58649

AN:

151894

Hom.:

13334

Cov.:

AF XY:

0.391

AC XY:

29025

AN XY:

74234

show subpopulations

African (AFR)

AF:

0.632

AC:

26158

AN:

41396

American (AMR)

AF:

0.294

AC:

4491

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.303

AC:

1053

AN:

3470

East Asian (EAS)

AF:

0.286

AC:

1469

AN:

5142

South Asian (SAS)

AF:

0.547

AC:

2635

AN:

4816

European-Finnish (FIN)

AF:

0.344

AC:

3621

AN:

10538

Middle Eastern (MID)

AF:

0.306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.265

AC:

18016

AN:

67942

Other (OTH)

AF:

0.375

AC:

792

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1617

3234

4852

6469

8086

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

548

1096

1644

2192

2740

<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:

0.317

Hom.:

2649

Bravo

AF:

0.388

Asia WGS

AF:

0.495

AC:

1719

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.0

(source)

DANN

Benign

0.44

PhyloP100

-0.76

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