3-179064233-C-T

Variant names:

• chr3-179064233-C-T
• rs4955793
• NM_022470.4:c.270+3250G>A

Variant summary

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

The NM_022470.4(ZMAT3):​c.270+3250G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 152,276 control chromosomes in the GnomAD database, including 554 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 0.077 (554 hom., cov: 33)
• Consequence: ZMAT3 NM_022470.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 7 publications found

Genes affected

ZMAT3 (HGNC:29983): (zinc finger matrin-type 3) This gene encodes a protein containing three zinc finger domains and a nuclear localization signal. The mRNA and the protein of this gene are upregulated by wildtype p53 and overexpression of this gene inhibits tumor cell growth, suggesting that this gene may have a role in the p53-dependent growth regulatory pathway. Alternative splicing of this gene results in two transcript variants encoding two isoforms differing in only one amino acid. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022470.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMAT3	NM_022470.4	MANE Select	c.270+3250G>A		intron	N/A	NP_071915.1
	ZMAT3	NM_001375824.1		c.270+3250G>A		intron	N/A	NP_001362753.1
	ZMAT3	NM_001375825.1		c.270+3250G>A		intron	N/A	NP_001362754.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMAT3	ENST00000311417.7	TSL:1 MANE Select	c.270+3250G>A		intron	N/A	ENSP00000311221.2
	ZMAT3	ENST00000652290.1		c.270+3250G>A		intron	N/A	ENSP00000498847.1
	ZMAT3	ENST00000432729.5	TSL:2	c.270+3250G>A		intron	N/A	ENSP00000396506.1

Frequencies

GnomAD3 genomes AF: 0.0773 AC: 11755 AN: 152158 Hom.: 554 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0749

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0751

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0772 AC: 11756 AN: 152276 Hom.: 554 Cov.: 33 AF XY: 0.0732 AC XY: 5451 AN XY: 74480

African (AFR) AF: 0.106 AC: 4406 AN: 41530

American (AMR) AF: 0.0747 AC: 1143 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0182 AC: 88 AN: 4826

European-Finnish (FIN) AF: 0.0222 AC: 236 AN: 10620

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0751 AC: 5107 AN: 68022

Other (OTH) AF: 0.101 AC: 213 AN: 2114

Alfa AF: 0.0786 Hom.: 952

Bravo AF: 0.0863

Asia WGS AF: 0.0170 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.62
PhyloP100		-0.23
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: rs4955793; hg19: chr3-178782021;