rs1317082

chr3-169779797-A-G

Variant summary

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

The NM_018657.5(MYNN):c.1060+236A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 494,428 control chromosomes in the GnomAD database, including 19,847 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 (4459 hom., cov: 32)
  • Exomes 𝑓: 0.28 (15388 hom.)
• Consequence: MYNN NM_018657.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYNN	NM_018657.5	c.1060+236A>G		intron_variant		ENST00000349841.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYNN	ENST00000349841.10	c.1060+236A>G		intron_variant		1	NM_018657.5	P1
	ENST00000602342.1	n.538T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32362 AN: 152040 Hom.: 4455 Cov.: 32

Gnomad AFR AF: 0.0657

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.228

GnomAD4 exome AF: 0.275 AC: 94188 AN: 342272 Hom.: 15388 Cov.: 4 AF XY: 0.275 AC XY: 48551 AN XY: 176560

Gnomad4 AFR exome AF: 0.0651

Gnomad4 AMR exome AF: 0.384

Gnomad4 ASJ exome AF: 0.180

Gnomad4 EAS exome AF: 0.621

Gnomad4 SAS exome AF: 0.268

Gnomad4 FIN exome AF: 0.277

Gnomad4 NFE exome AF: 0.244

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.213 AC: 32369 AN: 152156 Hom.: 4459 Cov.: 32 AF XY: 0.218 AC XY: 16206 AN XY: 74360

Gnomad4 AFR AF: 0.0657

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.226

Alfa AF: 0.244 Hom.: 7674

Bravo AF: 0.215

Asia WGS AF: 0.369 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
Cadd	Benign	2.3
Dann	Benign	0.93

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: rs1317082; hg19: chr3-169497585;