rs10104640

chr8-40785887-A-Cchr8-40785887-A-Gchr8-40785887-A-T

Variant summary

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

The NM_024645.3(ZMAT4):c.103-18157T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,030 control chromosomes in the GnomAD database, including 41,916 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 0.74 (41916 hom., cov: 31)
• Consequence: ZMAT4 NM_024645.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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 (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMAT4	NM_024645.3	c.103-18157T>G		intron_variant		ENST00000297737.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMAT4	ENST00000297737.11	c.103-18157T>G		intron_variant		2	NM_024645.3	P1

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112488 AN: 151912 Hom.: 41878 Cov.: 31

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.740 AC: 112576 AN: 152030 Hom.: 41916 Cov.: 31 AF XY: 0.741 AC XY: 55061 AN XY: 74318

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.742

Alfa AF: 0.728 Hom.: 7270

Bravo AF: 0.729

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.37

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: rs10104640; hg19: chr8-40643406;