NM_016132.5:c.162-110A>G

Variant names:

• chr15-48168949-T-C
• rs3817315
• NM_016132.5:c.162-110A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.79).
• 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 rank	MANE	Protein	UniProt
MYEF2	NM_016132.5	c.162-110A>G		intron_variant	Intron 1 of 16	ENST00000324324.12	NP_057216.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYEF2	ENST00000324324.12	c.162-110A>G		intron_variant	Intron 1 of 16	1	NM_016132.5	ENSP00000316950.7

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

African (AFR) AF: 0.418 AC: 6684 AN: 15988

American (AMR) AF: 0.821 AC: 16993 AN: 20690

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 15498 AN: 15506

East Asian (EAS) AF: 0.539 AC: 17343 AN: 32206

South Asian (SAS) AF: 0.868 AC: 42356 AN: 48794

European-Finnish (FIN) AF: 0.996 AC: 33056 AN: 33188

Middle Eastern (MID) AF: 0.980 AC: 2515 AN: 2566

European-Non Finnish (NFE) AF: 0.999 AC: 447225 AN: 447858

Other (OTH) AF: 0.909 AC: 29742 AN: 32736

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

African (AFR) AF: 0.435 AC: 18028 AN: 41480

American (AMR) AF: 0.833 AC: 12737 AN: 15286

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3469 AN: 3470

East Asian (EAS) AF: 0.520 AC: 2698 AN: 5184

South Asian (SAS) AF: 0.837 AC: 4029 AN: 4812

European-Finnish (FIN) AF: 0.996 AC: 10584 AN: 10628

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67889 AN: 68030

Other (OTH) AF: 0.837 AC: 1771 AN: 2116

Alfa AF: 0.853 Hom.: 8279

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
PhyloP100		1.3
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: rs3817315; hg19: chr15-48461146;