dbSNP rs2278418: ZNF350:c.238+46A>T (chr19-51968532-T-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.238+46A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 1,544,874 control chromosomes in the GnomAD database, including 27,643 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 ( 4985 hom., cov: 31)

Exomes 𝑓: 0.17 ( 22658 hom. )

Consequence

ZNF350
NM_021632.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.614

Publications

6 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF350	NM_021632.4 link	c.238+46A>T		intron_variant	Intron 4 of 4	ENST00000243644.9	NP_067645.3	Q9GZX5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF350	ENST00000243644.9 link	c.238+46A>T		intron_variant	Intron 4 of 4	1	NM_021632.4	ENSP00000243644.3		Q9GZX5

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35651

AN:

151832

Hom.:

4957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.378

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.189

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.283

Gnomad FIN

AF:

0.252

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.216

GnomAD2 exomes

AF:

0.203

AC:

50950

AN:

250848

AF XY:

0.201

show subpopulations

Gnomad AFR exome

AF:

0.380

Gnomad AMR exome

AF:

0.177

Gnomad ASJ exome

AF:

0.202

Gnomad EAS exome

AF:

0.222

Gnomad FIN exome

AF:

0.240

Gnomad NFE exome

AF:

0.159

Gnomad OTH exome

AF:

0.190

GnomAD4 exome

AF:

0.172

AC:

239707

AN:

1392924

Hom.:

22658

Cov.:

AF XY:

0.174

AC XY:

121393

AN XY:

696762

show subpopulations

African (AFR)

AF:

0.378

AC:

12059

AN:

31898

American (AMR)

AF:

0.183

AC:

8150

AN:

44640

Ashkenazi Jewish (ASJ)

AF:

0.199

AC:

5114

AN:

25682

East Asian (EAS)

AF:

0.229

AC:

9010

AN:

39326

South Asian (SAS)

AF:

0.262

AC:

22227

AN:

84710

European-Finnish (FIN)

AF:

0.231

AC:

12311

AN:

53228

Middle Eastern (MID)

AF:

0.163

AC:

922

AN:

5648

European-Non Finnish (NFE)

AF:

0.152

AC:

159241

AN:

1049740

Other (OTH)

AF:

0.184

AC:

10673

AN:

58052

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

8578

17156

25733

34311

42889

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5706

11412

17118

22824

28530

<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:

0.235

AC:

35741

AN:

151950

Hom.:

4985

Cov.:

AF XY:

0.239

AC XY:

17781

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.379

AC:

15668

AN:

41392

American (AMR)

AF:

0.189

AC:

2884

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.194

AC:

674

AN:

3468

East Asian (EAS)

AF:

0.222

AC:

1142

AN:

5152

South Asian (SAS)

AF:

0.284

AC:

1363

AN:

4806

European-Finnish (FIN)

AF:

0.252

AC:

2661

AN:

10572

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.158

AC:

10715

AN:

67970

Other (OTH)

AF:

0.220

AC:

464

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1306

2613

3919

5226

6532

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.200

Hom.:

608

Bravo

AF:

0.233

Asia WGS

AF:

0.308

AC:

1070

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.78

(source)

DANN

Benign

0.71

PhyloP100

-0.61

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over