XM_024446300.2:c.-824C>T

Variant names:

• chr6-44204326-C-T
• rs35131064
• XM_024446300.2:c.-824C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_024446300.2(MYMX):​c.-824C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,008 control chromosomes in the GnomAD database, including 3,283 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 0.19 (3283 hom., cov: 31)
• Consequence: MYMX XM_024446300.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 6 publications found

Genes affected

MYMX (HGNC:52391): (myomixer, myoblast fusion factor) Predicted to be involved in myoblast fusion involved in skeletal muscle regeneration; plasma membrane fusion; and skeletal muscle organ development. Predicted to be integral component of plasma membrane. Predicted to be active in Golgi membrane; endoplasmic reticulum membrane; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29461 AN: 151890 Hom.: 3285 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.231

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.194 AC: 29477 AN: 152008 Hom.: 3283 Cov.: 31 AF XY: 0.191 AC XY: 14154 AN XY: 74282

African (AFR) AF: 0.127 AC: 5253 AN: 41470

American (AMR) AF: 0.171 AC: 2604 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1479 AN: 3464

East Asian (EAS) AF: 0.0232 AC: 120 AN: 5172

South Asian (SAS) AF: 0.191 AC: 922 AN: 4820

European-Finnish (FIN) AF: 0.187 AC: 1968 AN: 10552

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16434 AN: 67962

Other (OTH) AF: 0.231 AC: 486 AN: 2102

Alfa AF: 0.196 Hom.: 2121

Bravo AF: 0.188

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.1
DANN	Benign	0.75
PhyloP100		0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs35131064; hg19: chr6-44172063;