rs3740329

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-42638638-C-A
• chr10-42638638-C-G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 7 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: 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	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.: 36

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

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

GnomAD4 genome AF: 0.232 AC: 35349 AN: 152300 Hom.: 4928 Cov.: 36 AF XY: 0.238 AC XY: 17716 AN XY: 74476

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: 57 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10037 AN: 68024

Other (OTH) AF: 0.218 AC: 461 AN: 2116

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
DANN	Benign	0.62
PhyloP100		-1.3
PromoterAI		0.15	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3740329; hg19: chr10-43134086;