chr8-40785887-A-C

Variant names:

• chr8-40785887-A-C
• rs10104640
• NM_024645.3:c.103-18157T>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.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
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024645.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMAT4	NM_024645.3	MANE Select	c.103-18157T>G		intron	N/A	NP_078921.1
	ZMAT4	NM_001135731.2		c.103-18157T>G		intron	N/A	NP_001129203.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMAT4	ENST00000297737.11	TSL:2 MANE Select	c.103-18157T>G		intron	N/A	ENSP00000297737.6
	ZMAT4	ENST00000315769.11	TSL:1	c.103-18157T>G		intron	N/A	ENSP00000319785.7
	ZMAT4	ENST00000958182.1		c.103-18157T>G		intron	N/A	ENSP00000628241.1

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

African (AFR) AF: 0.731 AC: 30262 AN: 41426

American (AMR) AF: 0.640 AC: 9768 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2763 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4635 AN: 5170

South Asian (SAS) AF: 0.747 AC: 3601 AN: 4822

European-Finnish (FIN) AF: 0.778 AC: 8217 AN: 10558

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50763 AN: 67998

Other (OTH) AF: 0.742 AC: 1568 AN: 2112

Alfa AF: 0.728 Hom.: 7270

Bravo AF: 0.729

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-1.1
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: rs10104640; hg19: chr8-40643406;