3-169788353-C-T

Variant names:

• chr3-169788353-C-T
• rs1920122
• NM_018657.5:c.*1675C>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.*1675C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,890 control chromosomes in the GnomAD database, including 8,931 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 0.33 (8931 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: MYNN NM_018657.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 17 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYNN	NM_018657.5	c.*1675C>T		3_prime_UTR_variant	Exon 8 of 8	ENST00000349841.10	NP_061127.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYNN	ENST00000349841.10	c.*1675C>T		3_prime_UTR_variant	Exon 8 of 8	1	NM_018657.5	ENSP00000326240.4
MYNN	ENST00000544106.5	c.*1675C>T		3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000440637.1

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50164 AN: 151772 Hom.: 8906 Cov.: 33

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.338

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.331 AC: 50238 AN: 151890 Hom.: 8931 Cov.: 33 AF XY: 0.334 AC XY: 24821 AN XY: 74214

African (AFR) AF: 0.391 AC: 16181 AN: 41414

American (AMR) AF: 0.394 AC: 6009 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3468

East Asian (EAS) AF: 0.685 AC: 3548 AN: 5182

South Asian (SAS) AF: 0.364 AC: 1756 AN: 4826

European-Finnish (FIN) AF: 0.275 AC: 2892 AN: 10530

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18062 AN: 67900

Other (OTH) AF: 0.342 AC: 719 AN: 2102

Alfa AF: 0.285 Hom.: 3629

Bravo AF: 0.349

Asia WGS AF: 0.512 AC: 1775 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.27
PhyloP100		0.43
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: rs1920122; hg19: chr3-169506141;