Genetic Variant ENSG00000285884:n.350C>G (chr10-42638638-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000737013.1(ENSG00000285884):n.350C>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 0.00000401 in 249,236 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 36)

Exomes 𝑓: 0.0000040 ( 0 hom. )

Consequence

ENSG00000285884
ENST00000737013.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.29

Publications

0 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: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000401

AC:

AN:

249236

Hom.:

AF XY:

0.00000695

AC XY:

AN XY:

143806

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

6234

American (AMR)

AF:

0.00

AC:

AN:

18526

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6978

East Asian (EAS)

AF:

0.00

AC:

AN:

8442

South Asian (SAS)

AF:

0.0000207

AC:

AN:

48386

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10532

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1070

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

137260

Other (OTH)

AF:

0.00

AC:

AN:

11808

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.2

(source)

DANN

Benign

0.42

PhyloP100

-1.3

PromoterAI

0.23

Neutral

(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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over