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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new If you want to explore the variant's impact on the transcript ENST00000737013.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737013.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF33B	NM_006955.3	MANE Select	c.-209G>T	upstream_gene	N/A	NP_008886.1	Q06732
ZNF33B	NM_001305033.2		c.-135G>T	upstream_gene	N/A	NP_001291962.1
ZNF33B	NM_001305035.2		c.-622G>T	upstream_gene	N/A	NP_001291964.1

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000285884	ENST00000737013.1	n.350C>A	non_coding_transcript_exon	Exon 1 of 2
ENSG00000285884	ENST00000737015.1	n.334C>A	non_coding_transcript_exon	Exon 1 of 2
ENSG00000285884	ENST00000737017.1	n.309C>A	non_coding_transcript_exon	Exon 1 of 2

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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