rs1317082

Variant names:

• chr3-169779797-A-G
• rs1317082
• NM_018657.5:c.1060+236A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 78 publications found

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]

ENSG00000269984 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MYNN	NM_018657.5	c.1060+236A>G		intron_variant	Intron 3 of 7	ENST00000349841.10	NP_061127.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYNN	ENST00000349841.10	c.1060+236A>G		intron_variant	Intron 3 of 7	1	NM_018657.5	ENSP00000326240.4

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

African (AFR) AF: 0.0651 AC: 721 AN: 11078

American (AMR) AF: 0.384 AC: 4992 AN: 12988

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 2064 AN: 11484

East Asian (EAS) AF: 0.621 AC: 16564 AN: 26678

South Asian (SAS) AF: 0.268 AC: 6327 AN: 23594

European-Finnish (FIN) AF: 0.277 AC: 6003 AN: 21680

Middle Eastern (MID) AF: 0.245 AC: 395 AN: 1614

European-Non Finnish (NFE) AF: 0.244 AC: 51864 AN: 212144

Other (OTH) AF: 0.250 AC: 5258 AN: 21012

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

African (AFR) AF: 0.0657 AC: 2727 AN: 41532

American (AMR) AF: 0.315 AC: 4820 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3470

East Asian (EAS) AF: 0.564 AC: 2910 AN: 5156

South Asian (SAS) AF: 0.260 AC: 1257 AN: 4826

European-Finnish (FIN) AF: 0.264 AC: 2788 AN: 10570

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16633 AN: 68002

Other (OTH) AF: 0.226 AC: 476 AN: 2108

Alfa AF: 0.241 Hom.: 18731

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
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1317082; hg19: chr3-169497585;