chr15-48175822-T-C

Variant names:

• chr15-48175822-T-C
• rs7163587
• NM_016132.5:c.161+2255A>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.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
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 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.161+2255A>G		intron	N/A	NP_057216.3
	MYEF2	NM_001301210.2		c.161+2255A>G		intron	N/A	NP_001288139.2
	MYEF2	NR_125408.2		n.219+2255A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYEF2	ENST00000324324.12	TSL:1 MANE Select	c.161+2255A>G		intron	N/A	ENSP00000316950.7
	MYEF2	ENST00000267836.10	TSL:1	c.161+2255A>G		intron	N/A	ENSP00000267836.6
	MYEF2	ENST00000561351.5	TSL:1	n.161+2255A>G		intron	N/A	ENSP00000453125.1

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

African (AFR) AF: 0.785 AC: 32577 AN: 41508

American (AMR) AF: 0.898 AC: 13725 AN: 15284

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

East Asian (EAS) AF: 0.924 AC: 4788 AN: 5182

South Asian (SAS) AF: 0.951 AC: 4583 AN: 4820

European-Finnish (FIN) AF: 0.998 AC: 10603 AN: 10622

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67954 AN: 67996

Other (OTH) AF: 0.946 AC: 1998 AN: 2112

Alfa AF: 0.950 Hom.: 20983

Bravo AF: 0.911

Asia WGS AF: 0.917 AC: 3188 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.57
DANN	Benign	0.40
PhyloP100		-0.27
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: rs7163587; hg19: chr15-48468019;