rs2722429

Positions:

• chr8-40625352-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZMAT4	NM_024645.3	c.578-44091A>G		intron_variant		ENST00000297737.11	NP_078921.1
ZMAT4	NM_001135731.2	c.350-44091A>G		intron_variant			NP_001129203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZMAT4	ENST00000297737.11	c.578-44091A>G		intron_variant		2	NM_024645.3	ENSP00000297737	P1
ZMAT4	ENST00000315769.11	c.350-44091A>G		intron_variant		1		ENSP00000319785
ZMAT4	ENST00000519406.5	c.578-44091A>G		intron_variant		3		ENSP00000428423

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

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.879

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.802

Alfa AF: 0.860 Hom.: 57153

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2722429; hg19: chr8-40482871;