6-44203747-A-T

Variant names:

• chr6-44203747-A-T
• rs7773444
• XM_024446300.2:c.-1403A>T

Variant summary

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

The XM_024446300.2(MYMX):​c.-1403A>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 0.845 in 152,184 control chromosomes in the GnomAD database, including 54,673 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 0.85 (54673 hom., cov: 32)
• Consequence: MYMX XM_024446300.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYMX	XM_024446300.2	c.-1403A>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: 0.845 AC: 128535 AN: 152066 Hom.: 54619 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.845 AC: 128644 AN: 152184 Hom.: 54673 Cov.: 32 AF XY: 0.844 AC XY: 62809 AN XY: 74404

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.892

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.859

Alfa AF: 0.812 Hom.: 2540

Bravo AF: 0.840

Asia WGS AF: 0.747 AC: 2598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7773444; hg19: chr6-44171484;