rs35131064

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYMX	XM_024446300.2	c.-824C>T		5_prime_UTR_variant	Exon 2 of 4		XP_024302068.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;