dbSNP rs3740329: ENSG00000285884:n.350C>A (chr10-42638638-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000737013.1(ENSG00000285884):n.350C>A 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 0.207 in 401,038 control chromosomes in the GnomAD database, including 10,137 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 0.23 ( 4928 hom., cov: 36)

Exomes 𝑓: 0.19 ( 5209 hom. )

Consequence

ENSG00000285884
ENST00000737013.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.29

Publications

7 publications found

Variant links:

Genes affected

ENSG00000285884 (HGNC:):

ENSG00000285884 links:

ZNF33B (HGNC:13097): (zinc finger protein 33B) This gene encodes a member of the zinc finger family of proteins. This gene shows decreased expression in cumulus cells derived from patients undergoing controlled ovarian stimulation. This gene is present in a gene cluster with several related zinc finger genes in the pericentromeric region of chromosome 10. Pseudogenes have been identified on chromosomes 7 and 10. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]

ZNF33B 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=-0.76).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF33B	NM_006955.3 link	c.-209G>T		upstream_gene_variant		ENST00000359467.8	NP_008886.1	Q06732

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF33B	ENST00000359467.8 link	c.-209G>T		upstream_gene_variant		1	NM_006955.3	ENSP00000352444.2		Q06732

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35288

AN:

152182

Hom.:

4908

Cov.:

show subpopulations

Gnomad AFR

AF:

0.386

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.216

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.306

Gnomad FIN

AF:

0.280

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.148

Gnomad OTH

AF:

0.216

GnomAD4 exome

AF:

0.191

AC:

47630

AN:

248738

Hom.:

5209

AF XY:

0.198

AC XY:

28457

AN XY:

143516

show subpopulations

African (AFR)

AF:

0.405

AC:

2513

AN:

6200

American (AMR)

AF:

0.176

AC:

3260

AN:

18490

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

1528

AN:

6968

East Asian (EAS)

AF:

0.128

AC:

1076

AN:

8434

South Asian (SAS)

AF:

0.289

AC:

13945

AN:

48244

European-Finnish (FIN)

AF:

0.253

AC:

2662

AN:

10502

Middle Eastern (MID)

AF:

0.200

AC:

214

AN:

1070

European-Non Finnish (NFE)

AF:

0.147

AC:

20159

AN:

137038

Other (OTH)

AF:

0.193

AC:

2273

AN:

11792

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1637

3274

4911

6548

8185

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

200

400

600

800

1000

<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:

0.232

AC:

35349

AN:

152300

Hom.:

4928

Cov.:

AF XY:

0.238

AC XY:

17716

AN XY:

74476

show subpopulations

African (AFR)

AF:

0.387

AC:

16080

AN:

41558

American (AMR)

AF:

0.176

AC:

2691

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.216

AC:

750

AN:

3472

East Asian (EAS)

AF:

0.125

AC:

647

AN:

5182

South Asian (SAS)

AF:

0.304

AC:

1467

AN:

4832

European-Finnish (FIN)

AF:

0.280

AC:

2969

AN:

10608

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.148

AC:

10037

AN:

68024

Other (OTH)

AF:

0.218

AC:

461

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1388

2776

4163

5551

6939

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:

0.195

Hom.:

546

Bravo

AF:

0.227

Asia WGS

AF:

0.223

AC:

777

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.1

(source)

DANN

Benign

0.62

PhyloP100

-1.3

PromoterAI

0.15

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(source)

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