3-169774313-C-T

Variant names:

• chr3-169774313-C-T
• rs10936599
• NM_018657.5:c.18C>T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_018657.5(MYNN):​c.18C>T​(p.His6His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 1,613,072 control chromosomes in the GnomAD database, including 58,494 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency:
  • Genomes: 𝑓 0.21 (4476 hom., cov: 32)
  • Exomes 𝑓: 0.26 (54018 hom.)
• Consequence: MYNN NM_018657.5 synonymous
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: 3.15
• Publications: 323 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 -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BP7: Synonymous conserved (PhyloP=3.15 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018657.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYNN	NM_018657.5	MANE Select	c.18C>T	p.His6His	synonymous	Exon 2 of 8	NP_061127.1
	MYNN	NM_001185118.2		c.18C>T	p.His6His	synonymous	Exon 3 of 9	NP_001172047.1
	MYNN	NM_001185119.1		c.18C>T	p.His6His	synonymous	Exon 1 of 6	NP_001172048.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYNN	ENST00000349841.10	TSL:1 MANE Select	c.18C>T	p.His6His	synonymous	Exon 2 of 8	ENSP00000326240.4
	MYNN	ENST00000356716.8	TSL:1	c.18C>T	p.His6His	synonymous	Exon 3 of 9	ENSP00000349150.3
	MYNN	ENST00000544106.5	TSL:1	c.18C>T	p.His6His	synonymous	Exon 1 of 6	ENSP00000440637.1

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32419 AN: 152062 Hom.: 4473 Cov.: 32

Gnomad AFR AF: 0.0657

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.227

GnomAD2 exomes AF: 0.291 AC: 73225 AN: 251364 AF XY: 0.284

Gnomad AFR exome AF: 0.0578

Gnomad AMR exome AF: 0.473

Gnomad ASJ exome AF: 0.181

Gnomad EAS exome AF: 0.561

Gnomad FIN exome AF: 0.269

Gnomad NFE exome AF: 0.245

Gnomad OTH exome AF: 0.276

GnomAD4 exome AF: 0.259 AC: 378152 AN: 1460892 Hom.: 54018 Cov.: 33 AF XY: 0.260 AC XY: 188774 AN XY: 726786

African (AFR) AF: 0.0531 AC: 1778 AN: 33470

American (AMR) AF: 0.456 AC: 20407 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 4748 AN: 26124

East Asian (EAS) AF: 0.608 AC: 24110 AN: 39680

South Asian (SAS) AF: 0.278 AC: 24014 AN: 86230

European-Finnish (FIN) AF: 0.274 AC: 14618 AN: 53406

Middle Eastern (MID) AF: 0.249 AC: 1434 AN: 5762

European-Non Finnish (NFE) AF: 0.245 AC: 271952 AN: 1111142

Other (OTH) AF: 0.250 AC: 15091 AN: 60358

GnomAD4 genome AF: 0.213 AC: 32425 AN: 152180 Hom.: 4476 Cov.: 32 AF XY: 0.218 AC XY: 16244 AN XY: 74402

African (AFR) AF: 0.0657 AC: 2729 AN: 41542

American (AMR) AF: 0.315 AC: 4816 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3466

East Asian (EAS) AF: 0.565 AC: 2921 AN: 5170

South Asian (SAS) AF: 0.269 AC: 1299 AN: 4828

European-Finnish (FIN) AF: 0.264 AC: 2796 AN: 10580

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

European-Non Finnish (NFE) AF: 0.245 AC: 16629 AN: 67996

Other (OTH) AF: 0.225 AC: 475 AN: 2110

Alfa AF: 0.242 Hom.: 23069

Bravo AF: 0.215

Asia WGS AF: 0.372 AC: 1293 AN: 3478

EpiCase AF: 0.242

EpiControl AF: 0.239

ClinVar

ClinVar submissions as Germline

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Chronic osteomyelitis (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		3.2
PromoterAI		0.0055	Neutral
Mutation Taster		=98/2	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10936599; hg19: chr3-169492101; COSMIC: COSV57753828; COSMIC: COSV57753828;