10-42638638-C-G

Variant names:

• chr10-42638638-C-G
• rs3740329
• ENST00000737013.1:n.350C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 0 publications found

Genes affected

ENSG00000285884 (HGNC:):

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: 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).

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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285884	ENST00000737013.1		n.350C>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000285884	ENST00000737015.1		n.334C>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000285884	ENST00000737017.1		n.309C>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 36

GnomAD4 exome AF: 0.00000401 AC: 1 AN: 249236 Hom.: 0 AF XY: 0.00000695 AC XY: 1 AN XY: 143806

African (AFR) AF: 0.00 AC: 0 AN: 6234

American (AMR) AF: 0.00 AC: 0 AN: 18526

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6978

East Asian (EAS) AF: 0.00 AC: 0 AN: 8442

South Asian (SAS) AF: 0.0000207 AC: 1 AN: 48386

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10532

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1070

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 137260

Other (OTH) AF: 0.00 AC: 0 AN: 11808

GnomAD4 genome Cov.: 36

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-1.3
PromoterAI		0.23	Neutral

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.

Other links and lift over

dbSNP: rs3740329;

hg19: chr10-43134086;