chr3-169788353-C-T

Position:

• chr3-169788353-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

MYNN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MYNN	NM_018657.5	c.*1675C>T		3_prime_UTR_variant	8/8	ENST00000349841.10	NP_061127.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYNN	ENST00000349841.10	c.*1675C>T		3_prime_UTR_variant	8/8	1	NM_018657.5	ENSP00000326240.4
MYNN	ENST00000544106.5	c.*1675C>T		3_prime_UTR_variant	6/6	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

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

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.342

Alfa AF: 0.281 Hom.: 1418

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

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: rs1920122; hg19: chr3-169506141;