chr8-40625302-G-A

Variant names:

• chr8-40625302-G-A
• rs2122950
• NM_024645.3:c.578-44041C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024645.3(ZMAT4):​c.578-44041C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0571 in 152,124 control chromosomes in the GnomAD database, including 425 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 0.057 (425 hom., cov: 32)
• Consequence: ZMAT4 NM_024645.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZMAT4	NM_024645.3	c.578-44041C>T		intron_variant	Intron 5 of 6	ENST00000297737.11	NP_078921.1
ZMAT4	NM_001135731.2	c.350-44041C>T		intron_variant	Intron 4 of 5		NP_001129203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZMAT4	ENST00000297737.11	c.578-44041C>T		intron_variant	Intron 5 of 6	2	NM_024645.3	ENSP00000297737.6
ZMAT4	ENST00000315769.11	c.350-44041C>T		intron_variant	Intron 4 of 5	1		ENSP00000319785.7
ZMAT4	ENST00000519406.5	c.578-44041C>T		intron_variant	Intron 5 of 5	3		ENSP00000428423.1

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8669 AN: 152006 Hom.: 422 Cov.: 32

Gnomad AFR AF: 0.0549

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0556

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

GnomAD4 genome AF: 0.0571 AC: 8686 AN: 152124 Hom.: 425 Cov.: 32 AF XY: 0.0598 AC XY: 4444 AN XY: 74374

African (AFR) AF: 0.0550 AC: 2281 AN: 41504

American (AMR) AF: 0.152 AC: 2314 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3466

East Asian (EAS) AF: 0.106 AC: 545 AN: 5158

South Asian (SAS) AF: 0.121 AC: 584 AN: 4826

European-Finnish (FIN) AF: 0.0284 AC: 301 AN: 10598

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0358 AC: 2435 AN: 67988

Other (OTH) AF: 0.0550 AC: 116 AN: 2110

Alfa AF: 0.0582 Hom.: 111

Bravo AF: 0.0678

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-0.67
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: rs2122950; hg19: chr8-40482821;