15-48153190-A-G

Variant names:

• chr15-48153190-A-G
• rs2675349
• NM_016132.5:c.1087+602T>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.1087+602T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,052 control chromosomes in the GnomAD database, including 7,785 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 (7785 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: MYEF2 NM_016132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYEF2	NM_016132.5	MANE Select	c.1087+602T>C		intron	N/A	NP_057216.3
	MYEF2	NM_001301210.2		c.1087+602T>C		intron	N/A	NP_001288139.2
	MYEF2	NR_125408.2		n.1694T>C		non_coding_transcript_exon	Exon 9 of 9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYEF2	ENST00000324324.12	TSL:1 MANE Select	c.1087+602T>C		intron	N/A	ENSP00000316950.7
	MYEF2	ENST00000267836.10	TSL:1	c.1087+602T>C		intron	N/A	ENSP00000267836.6
	MYEF2	ENST00000561351.5	TSL:1	n.*1249T>C		non_coding_transcript_exon	Exon 9 of 9	ENSP00000453125.1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29714 AN: 151934 Hom.: 7755 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.00415

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00209

Gnomad OTH AF: 0.155

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.196 AC: 29805 AN: 152052 Hom.: 7785 Cov.: 32 AF XY: 0.196 AC XY: 14609 AN XY: 74364

African (AFR) AF: 0.566 AC: 23424 AN: 41418

American (AMR) AF: 0.168 AC: 2558 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.000289 AC: 1 AN: 3466

East Asian (EAS) AF: 0.483 AC: 2499 AN: 5172

South Asian (SAS) AF: 0.163 AC: 788 AN: 4828

European-Finnish (FIN) AF: 0.00415 AC: 44 AN: 10612

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

European-Non Finnish (NFE) AF: 0.00209 AC: 142 AN: 67986

Other (OTH) AF: 0.164 AC: 345 AN: 2108

Alfa AF: 0.0587 Hom.: 766

Bravo AF: 0.226

Asia WGS AF: 0.403 AC: 1393 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.74
DANN	Benign	0.57
PhyloP100		-0.073
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: rs2675349; hg19: chr15-48445387;