ENST00000652290.1:c.1038-2755T>C

Variant names:

• chr3-178968251-A-G
• rs6797848
• ENST00000652290.1:c.1038-2755T>C

Variant summary

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

The ENST00000652290.1(ZMAT3):​c.1038-2755T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,226 control chromosomes in the GnomAD database, including 2,352 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 0.14 (2352 hom., cov: 33)
• Consequence: ZMAT3 ENST00000652290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354
• Publications: 4 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]

LOC124906307 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906307	XR_007096177.1	n.1974-1293T>C		intron_variant	Intron 1 of 3
LOC124906307	XR_007096178.1	n.2071-2755T>C		intron_variant	Intron 2 of 3
LOC124906307	XR_007096179.1	n.1974-2755T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZMAT3	ENST00000652290.1	c.1038-2755T>C		intron_variant	Intron 8 of 9			ENSP00000498847.1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21659 AN: 152108 Hom.: 2349 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.0545

Gnomad FIN AF: 0.0373

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0775

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.142 AC: 21679 AN: 152226 Hom.: 2352 Cov.: 33 AF XY: 0.141 AC XY: 10486 AN XY: 74430

African (AFR) AF: 0.268 AC: 11104 AN: 41504

American (AMR) AF: 0.140 AC: 2142 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3470

East Asian (EAS) AF: 0.393 AC: 2037 AN: 5178

South Asian (SAS) AF: 0.0541 AC: 261 AN: 4820

European-Finnish (FIN) AF: 0.0373 AC: 396 AN: 10616

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0775 AC: 5270 AN: 68020

Other (OTH) AF: 0.125 AC: 264 AN: 2116

Alfa AF: 0.0898 Hom.: 451

Bravo AF: 0.160

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.50
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs6797848; hg19: chr3-178686039;