15-48147301-A-G

Variant names:

• chr15-48147301-A-G
• rs2433359
• NM_016132.5:c.1639+1731T>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+1731T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0757 in 151,988 control chromosomes in the GnomAD database, including 1,168 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 0.076 (1168 hom., cov: 32)
• Consequence: MYEF2 NM_016132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYEF2	NM_016132.5	c.1639+1731T>C		intron_variant	Intron 16 of 16	ENST00000324324.12	NP_057216.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYEF2	ENST00000324324.12	c.1639+1731T>C		intron_variant	Intron 16 of 16	1	NM_016132.5	ENSP00000316950.7

Frequencies

GnomAD3 genomes AF: 0.0753 AC: 11437 AN: 151870 Hom.: 1154 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0755

Gnomad SAS AF: 0.0485

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000618

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0757 AC: 11498 AN: 151988 Hom.: 1168 Cov.: 32 AF XY: 0.0764 AC XY: 5680 AN XY: 74326

African (AFR) AF: 0.220 AC: 9133 AN: 41452

American (AMR) AF: 0.102 AC: 1562 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.0759 AC: 393 AN: 5180

South Asian (SAS) AF: 0.0484 AC: 233 AN: 4818

European-Finnish (FIN) AF: 0.00179 AC: 19 AN: 10614

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000619 AC: 42 AN: 67904

Other (OTH) AF: 0.0545 AC: 115 AN: 2110

Alfa AF: 0.0394 Hom.: 88

Bravo AF: 0.0907

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.8
DANN	Benign	0.43
PhyloP100		-0.25
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs2433359; hg19: chr15-48439498;