rs1823643

Positions:

• chr8-40657569-C-T

Variant summary

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

The NM_024645.3(ZMAT4):​c.577+17135G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,066 control chromosomes in the GnomAD database, including 55,110 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 0.84 (55110 hom., cov: 32)
• Consequence: ZMAT4 NM_024645.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMAT4	NM_024645.3	c.577+17135G>A		intron_variant		ENST00000297737.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMAT4	ENST00000297737.11	c.577+17135G>A		intron_variant		2	NM_024645.3	P1
ZMAT4	ENST00000315769.11	c.349+39676G>A		intron_variant		1
ZMAT4	ENST00000519406.5	c.577+17135G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128339 AN: 151948 Hom.: 55073 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.845 AC: 128433 AN: 152066 Hom.: 55110 Cov.: 32 AF XY: 0.846 AC XY: 62907 AN XY: 74342

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.899

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.920

Gnomad4 OTH AF: 0.866

Alfa AF: 0.905 Hom.: 58856

Bravo AF: 0.836

Asia WGS AF: 0.846 AC: 2931 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.38

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: rs1823643; hg19: chr8-40515088;