Variant chr8-40626720-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024645.3(ZMAT4):c.578-45459A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,122 control chromosomes in the GnomAD database, including 47,806 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 0.78 ( 47806 hom., cov: 32)

Consequence

ZMAT4
NM_024645.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32

Variant links:

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]

ZMAT4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZMAT4	NM_024645.3 link	c.578-45459A>G		intron_variant		ENST00000297737.11	NP_078921.1	Q9H898-1
ZMAT4	NM_001135731.2 link	c.350-45459A>G		intron_variant			NP_001129203.1	Q9H898-2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
ZMAT4	ENST00000297737.11 link	c.578-45459A>G	intron_variant	2	NM_024645.3	ENSP00000297737.6	Q9H898-1
ZMAT4	ENST00000315769.11 link	c.350-45459A>G	intron_variant	1		ENSP00000319785.7	Q9H898-2
ZMAT4	ENST00000519406.5 link	c.578-45459A>G	intron_variant	3		ENSP00000428423.1	E5RIF5

Frequencies

GnomAD3 genomes

AF:

0.784

AC:

119196

AN:

152004

Hom.:

47782

Cov.:

show subpopulations

Gnomad AFR

AF:

0.620

Gnomad AMI

AF:

0.768

Gnomad AMR

AF:

0.735

Gnomad ASJ

AF:

0.828

Gnomad EAS

AF:

0.721

Gnomad SAS

AF:

0.792

Gnomad FIN

AF:

0.877

Gnomad MID

AF:

0.848

Gnomad NFE

AF:

0.882

Gnomad OTH

AF:

0.810

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

GnomAD4 genome

AF:

0.784

AC:

119269

AN:

152122

Hom.:

47806

Cov.:

AF XY:

0.782

AC XY:

58196

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.620

Gnomad4 AMR

AF:

0.735

Gnomad4 ASJ

AF:

0.828

Gnomad4 EAS

AF:

0.721

Gnomad4 SAS

AF:

0.792

Gnomad4 FIN

AF:

0.877

Gnomad4 NFE

AF:

0.882

Gnomad4 OTH

AF:

0.811

Alfa

AF:

0.859

Hom.:

120328

Bravo

AF:

0.765

Asia WGS

AF:

0.761

AC:

2645

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.11

DANN

Benign

0.54

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over