rs3892388

Positions:

• chr9-34368986-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020702.5(MYORG):​c.*1813C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,182 control chromosomes in the GnomAD database, including 1,924 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 0.14 (1924 hom., cov: 32)
  • Exomes 𝑓: 0.21 (0 hom.)
• Consequence: MYORG NM_020702.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504

Genes affected

MYORG (HGNC:19918): (myogenesis regulating glycosidase (putative)) Predicted to enable hydrolase activity, hydrolyzing O-glycosyl compounds. Involved in skeletal muscle fiber development. Predicted to be located in endoplasmic reticulum membrane and nuclear membrane. Implicated in basal ganglia calcification. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYORG	NM_020702.5	c.*1813C>A		3_prime_UTR_variant	2/2	ENST00000297625.8	NP_065753.2
MYORG	XM_011517966.4	c.*1813C>A		3_prime_UTR_variant	2/2		XP_011516268.1
MYORG	XM_017014930.3	c.*1813C>A		3_prime_UTR_variant	2/2		XP_016870419.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYORG	ENST00000297625	c.*1813C>A		3_prime_UTR_variant	2/2	1	NM_020702.5	ENSP00000297625.8

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21666 AN: 152040 Hom.: 1921 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.160

GnomAD4 exome AF: 0.208 AC: 5 AN: 24 Hom.: 0 Cov.: 0 AF XY: 0.214 AC XY: 3 AN XY: 14

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.222

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.142 AC: 21676 AN: 152158 Hom.: 1924 Cov.: 32 AF XY: 0.144 AC XY: 10705 AN XY: 74376

Gnomad4 AFR AF: 0.0458

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.163

Alfa AF: 0.167 Hom.: 292

Bravo AF: 0.133

Asia WGS AF: 0.274 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.65
DANN	Benign	0.39
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs3892388; hg19: chr9-34368984; COSMIC: COSV52628244; COSMIC: COSV52628244;