rs4736884

chr8-40882173-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024645.3(ZMAT4):c.-5+15510C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,056 control chromosomes in the GnomAD database, including 3,624 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 0.22 (3624 hom., cov: 32)
• Consequence: ZMAT4 NM_024645.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMAT4	NM_024645.3	c.-5+15510C>T		intron_variant		ENST00000297737.11
ZMAT4	NM_001135731.2	c.-5+15510C>T		intron_variant
ZMAT4	XM_017013836.3	c.-5+15510C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMAT4	ENST00000297737.11	c.-5+15510C>T		intron_variant		2	NM_024645.3	P1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32810 AN: 151936 Hom.: 3610 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0794

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.216 AC: 32856 AN: 152056 Hom.: 3624 Cov.: 32 AF XY: 0.215 AC XY: 15955 AN XY: 74316

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.0792

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.209

Alfa AF: 0.229 Hom.: 659

Bravo AF: 0.220

Asia WGS AF: 0.115 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.49
Dann	Benign	0.62

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: rs4736884; hg19: chr8-40739692;