rs3772190

chr3-169782699-G-Achr3-169782699-G-C

Variant summary

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

The NM_018657.5(MYNN):c.1399+56G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,455,106 control chromosomes in the GnomAD database, including 52,129 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 0.21 (4457 hom., cov: 32)
  • Exomes 𝑓: 0.26 (47672 hom.)
• Consequence: MYNN NM_018657.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

Genes affected

MYNN (HGNC:14955): (myoneurin) This gene encodes a member of the BTB/POZ and zinc finger domain-containing protein family that are involved in the control of gene expression. Alternative splicing results in multiple transcript variants and a pseudogene has been identified on chromosome 14. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYNN	NM_018657.5	c.1399+56G>A		intron_variant		ENST00000349841.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYNN	ENST00000349841.10	c.1399+56G>A		intron_variant		1	NM_018657.5	P1

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32325 AN: 151972 Hom.: 4453 Cov.: 32

Gnomad AFR AF: 0.0649

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.228

GnomAD4 exome AF: 0.258 AC: 336655 AN: 1303016 Hom.: 47672 AF XY: 0.259 AC XY: 169021 AN XY: 652212

Gnomad4 AFR exome AF: 0.0521

Gnomad4 AMR exome AF: 0.432

Gnomad4 ASJ exome AF: 0.183

Gnomad4 EAS exome AF: 0.611

Gnomad4 SAS exome AF: 0.269

Gnomad4 FIN exome AF: 0.273

Gnomad4 NFE exome AF: 0.246

Gnomad4 OTH exome AF: 0.251

GnomAD4 genome AF: 0.213 AC: 32331 AN: 152090 Hom.: 4457 Cov.: 32 AF XY: 0.218 AC XY: 16217 AN XY: 74364

Gnomad4 AFR AF: 0.0648

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.226

Alfa AF: 0.153 Hom.: 413

Bravo AF: 0.214

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	11
Dann	Benign	0.60

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: rs3772190; hg19: chr3-169500487;