15-48146720-A-G

Variant names:

• chr15-48146720-A-G
• rs16960631
• NM_016132.5:c.1639+2312T>C

Variant summary

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

The NM_016132.5(MYEF2):​c.1639+2312T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.012 in 152,096 control chromosomes in the GnomAD database, including 151 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 0.012 (151 hom., cov: 32)
• Consequence: MYEF2 NM_016132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016132.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYEF2	NM_016132.5	MANE Select	c.1639+2312T>C		intron	N/A	NP_057216.3
	MYEF2	NM_001301210.2		c.1567+2312T>C		intron	N/A	NP_001288139.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYEF2	ENST00000324324.12	TSL:1 MANE Select	c.1639+2312T>C		intron	N/A	ENSP00000316950.7
	MYEF2	ENST00000267836.10	TSL:1	c.1567+2312T>C		intron	N/A	ENSP00000267836.6
	MYEF2	ENST00000620867.4	TSL:1	c.472+2312T>C		intron	N/A	ENSP00000480281.1

Frequencies

GnomAD3 genomes AF: 0.0119 AC: 1813 AN: 151978 Hom.: 147 Cov.: 32

Gnomad AFR AF: 0.00536

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0127

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0120 AC: 1823 AN: 152096 Hom.: 151 Cov.: 32 AF XY: 0.0133 AC XY: 990 AN XY: 74346

African (AFR) AF: 0.00532 AC: 221 AN: 41556

American (AMR) AF: 0.0127 AC: 194 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.225 AC: 1164 AN: 5168

South Asian (SAS) AF: 0.0360 AC: 174 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10630

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000309 AC: 21 AN: 67886

Other (OTH) AF: 0.0232 AC: 49 AN: 2112

Alfa AF: 0.00407 Hom.: 2

Bravo AF: 0.0136

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.3
DANN	Benign	0.69
PhyloP100		0.37
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.13		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: rs16960631; hg19: chr15-48438917;