rs6709245

chr2-131491303-A-G

Variant summary

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

The NM_001085365.2(MZT2A):c.319+573T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 287,440 control chromosomes in the GnomAD database, including 26,338 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 0.44 (17041 hom., cov: 32)
  • Exomes 𝑓: 0.34 (9297 hom.)
• Consequence: MZT2A NM_001085365.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630

Genes affected

MZT2A (HGNC:33187): (mitotic spindle organizing protein 2A) Located in centrosome; cytosol; and nucleoplasm. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MZT2A	NM_001085365.2	c.319+573T>C		intron_variant		ENST00000309451.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MZT2A	ENST00000309451.7	c.319+573T>C		intron_variant		1	NM_001085365.2	P1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66075 AN: 151600 Hom.: 16987 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.447

GnomAD4 exome AF: 0.339 AC: 46008 AN: 135724 Hom.: 9297 Cov.: 0 AF XY: 0.344 AC XY: 24610 AN XY: 71618

Gnomad4 AFR exome AF: 0.651

Gnomad4 AMR exome AF: 0.592

Gnomad4 ASJ exome AF: 0.394

Gnomad4 EAS exome AF: 0.755

Gnomad4 SAS exome AF: 0.387

Gnomad4 FIN exome AF: 0.315

Gnomad4 NFE exome AF: 0.264

Gnomad4 OTH exome AF: 0.331

GnomAD4 genome AF: 0.436 AC: 66197 AN: 151716 Hom.: 17041 Cov.: 32 AF XY: 0.444 AC XY: 32911 AN XY: 74128

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.453

Alfa AF: 0.315 Hom.: 10351

Bravo AF: 0.467

Asia WGS AF: 0.583 AC: 2025 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	4.7
Dann	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs6709245; hg19: chr2-132248876;