rs722103

chr8-40641600-G-A

Variant summary

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

The NM_024645.3(ZMAT4):c.577+33104C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0638 in 152,174 control chromosomes in the GnomAD database, including 718 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 0.064 (718 hom., cov: 33)
• Consequence: ZMAT4 NM_024645.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558

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]

LOC107986938 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMAT4	NM_024645.3	c.577+33104C>T		intron_variant		ENST00000297737.11
LOC107986938	XR_007060896.1	n.3932-1577G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMAT4	ENST00000297737.11	c.577+33104C>T		intron_variant		2	NM_024645.3	P1
ZMAT4	ENST00000315769.11	c.349+55645C>T		intron_variant		1
ZMAT4	ENST00000519406.5	c.577+33104C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0638 AC: 9699 AN: 152056 Hom.: 717 Cov.: 33

Gnomad AFR AF: 0.0617

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0902

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0621

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0302

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0638 AC: 9710 AN: 152174 Hom.: 718 Cov.: 33 AF XY: 0.0682 AC XY: 5073 AN XY: 74396

Gnomad4 AFR AF: 0.0619

Gnomad4 AMR AF: 0.0905

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0621

Gnomad4 NFE AF: 0.0302

Gnomad4 OTH AF: 0.0652

Alfa AF: 0.0446 Hom.: 37

Bravo AF: 0.0678

Asia WGS AF: 0.244 AC: 844 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.26
Dann	Benign	0.19

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: rs722103; hg19: chr8-40499119;