rs3772190

Variant names:

• chr3-169782699-G-A
• rs3772190
• NM_018657.5:c.1399+56G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-169782699-G-A
• chr3-169782699-G-C
• chr3-169782699-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 43 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MYNN	NM_018657.5	c.1399+56G>A		intron_variant	Intron 5 of 7	ENST00000349841.10	NP_061127.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYNN	ENST00000349841.10	c.1399+56G>A		intron_variant	Intron 5 of 7	1	NM_018657.5	ENSP00000326240.4

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

African (AFR) AF: 0.0521 AC: 1466 AN: 28154

American (AMR) AF: 0.432 AC: 12901 AN: 29842

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 4288 AN: 23392

East Asian (EAS) AF: 0.611 AC: 23171 AN: 37940

South Asian (SAS) AF: 0.269 AC: 19367 AN: 71974

European-Finnish (FIN) AF: 0.273 AC: 12953 AN: 47456

Middle Eastern (MID) AF: 0.252 AC: 1294 AN: 5132

European-Non Finnish (NFE) AF: 0.246 AC: 247511 AN: 1004530

Other (OTH) AF: 0.251 AC: 13704 AN: 54596

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

African (AFR) AF: 0.0648 AC: 2690 AN: 41512

American (AMR) AF: 0.316 AC: 4824 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3470

East Asian (EAS) AF: 0.565 AC: 2925 AN: 5178

South Asian (SAS) AF: 0.260 AC: 1253 AN: 4822

European-Finnish (FIN) AF: 0.264 AC: 2799 AN: 10584

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

European-Non Finnish (NFE) AF: 0.244 AC: 16603 AN: 67932

Other (OTH) AF: 0.226 AC: 477 AN: 2112

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
PhyloP100		-0.15
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: rs3772190; hg19: chr3-169500487; COSMIC: COSV107440339; COSMIC: COSV107440339;