rs2722429

Variant names:

• chr8-40625352-T-C
• rs2722429
• NM_024645.3:c.578-44091A>G

Variant summary

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

The NM_024645.3(ZMAT4):​c.578-44091A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 151,960 control chromosomes in the GnomAD database, including 47,638 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 0.78 (47638 hom., cov: 31)
• Consequence: ZMAT4 NM_024645.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 3 publications found

Genes affected

ZMAT4 (HGNC:25844): (zinc finger matrin-type 4) Enables identical protein binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZMAT4	NM_024645.3	c.578-44091A>G		intron_variant	Intron 5 of 6	ENST00000297737.11	NP_078921.1
ZMAT4	NM_001135731.2	c.350-44091A>G		intron_variant	Intron 4 of 5		NP_001129203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZMAT4	ENST00000297737.11	c.578-44091A>G		intron_variant	Intron 5 of 6	2	NM_024645.3	ENSP00000297737.6
ZMAT4	ENST00000315769.11	c.350-44091A>G		intron_variant	Intron 4 of 5	1		ENSP00000319785.7
ZMAT4	ENST00000519406.5	c.578-44091A>G		intron_variant	Intron 5 of 5	3		ENSP00000428423.1

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118704 AN: 151844 Hom.: 47613 Cov.: 31

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.782 AC: 118779 AN: 151960 Hom.: 47638 Cov.: 31 AF XY: 0.781 AC XY: 57988 AN XY: 74264

African (AFR) AF: 0.600 AC: 24832 AN: 41394

American (AMR) AF: 0.748 AC: 11428 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2872 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3705 AN: 5140

South Asian (SAS) AF: 0.800 AC: 3853 AN: 4814

European-Finnish (FIN) AF: 0.879 AC: 9290 AN: 10568

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.885 AC: 60133 AN: 67984

Other (OTH) AF: 0.802 AC: 1688 AN: 2106

Alfa AF: 0.838 Hom.: 86492

Bravo AF: 0.763

Asia WGS AF: 0.766 AC: 2664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.2
DANN	Benign	0.79
PhyloP100		0.032
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: rs2722429; hg19: chr8-40482871;