rs2459394

chr15-48152551-T-Achr15-48152551-T-G

Variant summary

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

The NM_016132.5(MYEF2):c.1088-267A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 383,508 control chromosomes in the GnomAD database, including 11,196 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 0.20 (7810 hom., cov: 32)
  • Exomes 𝑓: 0.074 (3386 hom.)
• Consequence: MYEF2 NM_016132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

Genes affected

MYEF2 (HGNC:17940): (myelin expression factor 2) Enables RNA binding activity. Involved in myotube differentiation and neuron differentiation. Located in nucleus. [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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYEF2	NM_016132.5	c.1088-267A>T		intron_variant		ENST00000324324.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYEF2	ENST00000324324.12	c.1088-267A>T		intron_variant		1	NM_016132.5	P4

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30187 AN: 151788 Hom.: 7780 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.00577

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.00632

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00787

Gnomad OTH AF: 0.161

GnomAD4 exome AF: 0.0736 AC: 17036 AN: 231606 Hom.: 3386 Cov.: 0 AF XY: 0.0698 AC XY: 8280 AN XY: 118550

Gnomad4 AFR exome AF: 0.558

Gnomad4 AMR exome AF: 0.181

Gnomad4 ASJ exome AF: 0.00434

Gnomad4 EAS exome AF: 0.450

Gnomad4 SAS exome AF: 0.129

Gnomad4 FIN exome AF: 0.00662

Gnomad4 NFE exome AF: 0.00729

Gnomad4 OTH exome AF: 0.0970

GnomAD4 genome AF: 0.199 AC: 30277 AN: 151902 Hom.: 7810 Cov.: 32 AF XY: 0.200 AC XY: 14831 AN XY: 74270

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.00577

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.00632

Gnomad4 NFE AF: 0.00787

Gnomad4 OTH AF: 0.170

Alfa AF: 0.111 Hom.: 517

Bravo AF: 0.229

Asia WGS AF: 0.404 AC: 1399 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	11
Dann	Benign	0.86

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: rs2459394; hg19: chr15-48444748;