chr10-42633432-A-G

Variant names:

• chr10-42633432-A-G
• rs209390
• NM_006955.3:c.10-993T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006955.3(ZNF33B):​c.10-993T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,084 control chromosomes in the GnomAD database, including 46,976 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 0.78 (46976 hom., cov: 32)
• Consequence: ZNF33B NM_006955.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 5 publications found

Genes affected

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006955.3. 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
	ZNF33B	NM_006955.3	MANE Select	c.10-993T>C		intron	N/A	NP_008886.1	Q06732
	ZNF33B	NM_001305033.2		c.31-993T>C		intron	N/A	NP_001291962.1
	ZNF33B	NM_001305035.2		c.-404-993T>C		intron	N/A	NP_001291964.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF33B	ENST00000359467.8	TSL:1 MANE Select	c.10-993T>C		intron	N/A	ENSP00000352444.2	Q06732
	ZNF33B	ENST00000876416.1		c.10-993T>C		intron	N/A	ENSP00000546475.1
	ZNF33B	ENST00000876415.1		c.10-993T>C		intron	N/A	ENSP00000546474.1

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118525 AN: 151966 Hom.: 46967 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.797

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.780 AC: 118576 AN: 152084 Hom.: 46976 Cov.: 32 AF XY: 0.775 AC XY: 57623 AN XY: 74342

African (AFR) AF: 0.633 AC: 26263 AN: 41458

American (AMR) AF: 0.827 AC: 12631 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2742 AN: 3470

East Asian (EAS) AF: 0.962 AC: 4976 AN: 5172

South Asian (SAS) AF: 0.769 AC: 3705 AN: 4818

European-Finnish (FIN) AF: 0.720 AC: 7610 AN: 10570

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58015 AN: 68010

Other (OTH) AF: 0.798 AC: 1677 AN: 2102

Alfa AF: 0.831 Hom.: 146530

Bravo AF: 0.784

Asia WGS AF: 0.848 AC: 2947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		0.044
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs209390; hg19: chr10-43128880;