Genetic Variant ZNF350:c.*285C>T (chr19-51964569-G-A) – 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.*285C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 427,122 control chromosomes in the GnomAD database, including 4,474 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 0.12 ( 1314 hom., cov: 32)

Exomes 𝑓: 0.14 ( 3160 hom. )

Consequence

ZNF350
NM_021632.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.535

Publications

12 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:

Genome browser will be placed here

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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 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.*285C>T		3_prime_UTR	Exon 5 of 5	NP_067645.3
	ZNF350-AS1	NR_103847.1		n.103-11822G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF350	ENST00000243644.9	TSL:1 MANE Select	c.*285C>T	3_prime_UTR	Exon 5 of 5	ENSP00000243644.3	Q9GZX5
ZNF350-AS1	ENST00000595010.5	TSL:1	n.125-11822G>A	intron	N/A
ZNF350	ENST00000853589.1		c.*285C>T	3_prime_UTR	Exon 6 of 6	ENSP00000523648.1

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17863

AN:

151956

Hom.:

1315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0468

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.219

Gnomad SAS

AF:

0.261

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.114

GnomAD4 exome

AF:

0.142

AC:

39044

AN:

275048

Hom.:

3160

Cov.:

AF XY:

0.146

AC XY:

20867

AN XY:

142876

show subpopulations

African (AFR)

AF:

0.0421

AC:

351

AN:

8328

American (AMR)

AF:

0.139

AC:

1321

AN:

9494

Ashkenazi Jewish (ASJ)

AF:

0.0970

AC:

884

AN:

9116

East Asian (EAS)

AF:

0.228

AC:

4309

AN:

18934

South Asian (SAS)

AF:

0.228

AC:

5213

AN:

22856

European-Finnish (FIN)

AF:

0.160

AC:

2846

AN:

17738

Middle Eastern (MID)

AF:

0.128

AC:

162

AN:

1268

European-Non Finnish (NFE)

AF:

0.129

AC:

21994

AN:

170816

Other (OTH)

AF:

0.119

AC:

1964

AN:

16498

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1555

3110

4664

6219

7774

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

172

344

516

688

860

<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:

0.117

AC:

17868

AN:

152074

Hom.:

1314

Cov.:

AF XY:

0.124

AC XY:

9203

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.0467

AC:

1939

AN:

41480

American (AMR)

AF:

0.125

AC:

1911

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

349

AN:

3472

East Asian (EAS)

AF:

0.220

AC:

1133

AN:

5154

South Asian (SAS)

AF:

0.261

AC:

1254

AN:

4802

European-Finnish (FIN)

AF:

0.185

AC:

1954

AN:

10568

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.131

AC:

8932

AN:

67986

Other (OTH)

AF:

0.116

AC:

246

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

788

1577

2365

3154

3942

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

218

436

654

872

1090

<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:

0.128

Hom.:

1409

Bravo

AF:

0.104

Asia WGS

AF:

0.253

AC:

876

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.7

(source)

DANN

Benign

0.28

PhyloP100

-0.54

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