dbSNP rs11595684: ZNF33BP1:n.1234A>G (chr10-37794876-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 ENST00000452497.1(ZNF33BP1):n.1234A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 154,572 control chromosomes in the GnomAD database, including 1,174 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 0.11 ( 1161 hom., cov: 33)

Exomes 𝑓: 0.10 ( 13 hom. )

Consequence

ZNF33BP1
ENST00000452497.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.72

Publications

0 publications found

Variant links:

Genes affected

ZNF33BP1 (HGNC:44975): (zinc finger protein 33B pseudogene 1)

ZNF33BP1 links:

ZNF248 (HGNC:13041): (zinc finger protein 248) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF248 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=-0.86).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
ZNF33BP1	NR_051997.1 link	n.300A>G	non_coding_transcript_exon_variant	Exon 1 of 1
ZNF248	NM_001267607.3 link	c.331-18301A>G	intron_variant	Intron 6 of 6	NP_001254536.1	A0A087WTK3
ZNF248	NM_001352476.2 link	c.331-18301A>G	intron_variant	Intron 5 of 5	NP_001339405.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF33BP1	ENST00000452497.1 link	n.1234A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ZNF248	ENST00000615949.6 link	c.331-18301A>G		intron_variant	Intron 6 of 6	5		ENSP00000477940.1		A0A087WTK3

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16672

AN:

152150

Hom.:

1160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0381

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.105

Gnomad SAS

AF:

0.0635

Gnomad FIN

AF:

0.0930

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.133

GnomAD4 exome

AF:

0.101

AC:

232

AN:

2304

Hom.:

Cov.:

AF XY:

0.0953

AC XY:

117

AN XY:

1228

show subpopulations

African (AFR)

AF:

0.100

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.125

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0935

AC:

164

AN:

1754

Middle Eastern (MID)

AF:

0.200

AC:

AN:

European-Non Finnish (NFE)

AF:

0.131

AC:

AN:

420

Other (OTH)

AF:

0.0862

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.110

AC:

16674

AN:

152268

Hom.:

1161

Cov.:

AF XY:

0.110

AC XY:

8183

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.0382

AC:

1587

AN:

41580

American (AMR)

AF:

0.187

AC:

2863

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

482

AN:

3472

East Asian (EAS)

AF:

0.105

AC:

542

AN:

5170

South Asian (SAS)

AF:

0.0631

AC:

305

AN:

4830

European-Finnish (FIN)

AF:

0.0930

AC:

987

AN:

10608

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.139

AC:

9475

AN:

68002

Other (OTH)

AF:

0.132

AC:

279

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

750

1499

2249

2998

3748

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<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:

0.118

Hom.:

147

Bravo

AF:

0.118

Asia WGS

AF:

0.0830

AC:

287

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

4.1

(source)

DANN

Benign

0.71

PhyloP100

-5.7

Splicing

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