chr15-48152551-T-A

Variant names:

• chr15-48152551-T-A
• rs2459394
• ENST00000561351.5:n.*1888A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561351.5(MYEF2):​n.*1888A>T variant causes a non coding transcript exon 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 ENST00000561351.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MYEF2	NM_016132.5	c.1088-267A>T		intron_variant	Intron 10 of 16	ENST00000324324.12	NP_057216.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYEF2	ENST00000324324.12	c.1088-267A>T		intron_variant	Intron 10 of 16	1	NM_016132.5	ENSP00000316950.7

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

African (AFR) AF: 0.558 AC: 3458 AN: 6196

American (AMR) AF: 0.181 AC: 1443 AN: 7952

Ashkenazi Jewish (ASJ) AF: 0.00434 AC: 36 AN: 8296

East Asian (EAS) AF: 0.450 AC: 8356 AN: 18574

South Asian (SAS) AF: 0.129 AC: 1060 AN: 8238

European-Finnish (FIN) AF: 0.00662 AC: 119 AN: 17982

Middle Eastern (MID) AF: 0.0188 AC: 22 AN: 1168

European-Non Finnish (NFE) AF: 0.00729 AC: 1079 AN: 148110

Other (OTH) AF: 0.0970 AC: 1463 AN: 15090

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

African (AFR) AF: 0.567 AC: 23470 AN: 41402

American (AMR) AF: 0.168 AC: 2552 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.00577 AC: 20 AN: 3468

East Asian (EAS) AF: 0.482 AC: 2483 AN: 5154

South Asian (SAS) AF: 0.164 AC: 788 AN: 4814

European-Finnish (FIN) AF: 0.00632 AC: 67 AN: 10602

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00787 AC: 535 AN: 67944

Other (OTH) AF: 0.170 AC: 358 AN: 2108

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
PhyloP100		1.2
PromoterAI		0.0034	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2459394; hg19: chr15-48444748;