rs3817315

chr15-48168949-T-C

Variant summary

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

The NM_016132.5(MYEF2):c.162-110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 801,744 control chromosomes in the GnomAD database, including 348,520 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 0.80 (54079 hom., cov: 32)
  • Exomes 𝑓: 0.94 (294441 hom.)
• Consequence: MYEF2 NM_016132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYEF2	NM_016132.5	c.162-110A>G		intron_variant		ENST00000324324.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYEF2	ENST00000324324.12	c.162-110A>G		intron_variant		1	NM_016132.5	P4

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122380 AN: 152094 Hom.: 54081 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.846

GnomAD4 exome AF: 0.941 AC: 611412 AN: 649532 Hom.: 294441 AF XY: 0.942 AC XY: 317248 AN XY: 336944

Gnomad4 AFR exome AF: 0.418

Gnomad4 AMR exome AF: 0.821

Gnomad4 ASJ exome AF: 0.999

Gnomad4 EAS exome AF: 0.539

Gnomad4 SAS exome AF: 0.868

Gnomad4 FIN exome AF: 0.996

Gnomad4 NFE exome AF: 0.999

Gnomad4 OTH exome AF: 0.909

GnomAD4 genome AF: 0.804 AC: 122407 AN: 152212 Hom.: 54079 Cov.: 32 AF XY: 0.804 AC XY: 59834 AN XY: 74436

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.837

Alfa AF: 0.868 Hom.: 8203

Bravo AF: 0.775

Asia WGS AF: 0.599 AC: 2090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	12
Dann	Benign	0.81

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: rs3817315; hg19: chr15-48461146;