chr15-48175822-T-C

Position:

• chr15-48175822-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.161+2255A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,200 control chromosomes in the GnomAD database, including 65,922 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 0.93 (65922 hom., cov: 32)
• Consequence: MYEF2 NM_016132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268

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]

MYEF2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYEF2	NM_016132.5	c.161+2255A>G		intron_variant		ENST00000324324.12	NP_057216.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYEF2	ENST00000324324.12	c.161+2255A>G		intron_variant		1	NM_016132.5	ENSP00000316950.7

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140846 AN: 152082 Hom.: 65910 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.946

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

GnomAD4 genome AF: 0.926 AC: 140903 AN: 152200 Hom.: 65922 Cov.: 32 AF XY: 0.925 AC XY: 68849 AN XY: 74422

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.999

Gnomad4 OTH AF: 0.946

Alfa AF: 0.949 Hom.: 9228

Bravo AF: 0.911

Asia WGS AF: 0.917 AC: 3188 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.57
DANN	Benign	0.40

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: rs7163587; hg19: chr15-48468019;