chr6-44203747-A-T

Variant names:

• chr6-44203747-A-T
• rs7773444
• XM_024446300.2:c.-1403A>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.-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
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 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: 0.845 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

African (AFR) AF: 0.907 AC: 37659 AN: 41536

American (AMR) AF: 0.753 AC: 11506 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3095 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3399 AN: 5166

South Asian (SAS) AF: 0.793 AC: 3824 AN: 4820

European-Finnish (FIN) AF: 0.887 AC: 9403 AN: 10600

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56998 AN: 68000

Other (OTH) AF: 0.859 AC: 1812 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7773444; hg19: chr6-44171484;