chr15-48152551-T-A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000561351.5(MYEF2):​n.*1888A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 383,508 control chromosomes in the GnomAD database, including 11,196 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 ( 7810 hom., cov: 32)
Exomes 𝑓: 0.074 ( 3386 hom. )

Consequence

MYEF2
ENST00000561351.5 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.22

Publications

3 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MYEF2NM_016132.5 linkc.1088-267A>T intron_variant Intron 10 of 16 ENST00000324324.12 NP_057216.3 Q9P2K5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MYEF2ENST00000324324.12 linkc.1088-267A>T intron_variant Intron 10 of 16 1 NM_016132.5 ENSP00000316950.7 A0A0A0MR39

Frequencies

GnomAD3 genomes
AF:
0.199
AC:
30187
AN:
151788
Hom.:
7780
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.567
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.167
Gnomad ASJ
AF:
0.00577
Gnomad EAS
AF:
0.482
Gnomad SAS
AF:
0.165
Gnomad FIN
AF:
0.00632
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.00787
Gnomad OTH
AF:
0.161
GnomAD4 exome
AF:
0.0736
AC:
17036
AN:
231606
Hom.:
3386
Cov.:
0
AF XY:
0.0698
AC XY:
8280
AN XY:
118550
show subpopulations
African (AFR)
AF:
0.558
AC:
3458
AN:
6196
American (AMR)
AF:
0.181
AC:
1443
AN:
7952
Ashkenazi Jewish (ASJ)
AF:
0.00434
AC:
36
AN:
8296
East Asian (EAS)
AF:
0.450
AC:
8356
AN:
18574
South Asian (SAS)
AF:
0.129
AC:
1060
AN:
8238
European-Finnish (FIN)
AF:
0.00662
AC:
119
AN:
17982
Middle Eastern (MID)
AF:
0.0188
AC:
22
AN:
1168
European-Non Finnish (NFE)
AF:
0.00729
AC:
1079
AN:
148110
Other (OTH)
AF:
0.0970
AC:
1463
AN:
15090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
483
965
1448
1930
2413
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
96
192
288
384
480
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.199
AC:
30277
AN:
151902
Hom.:
7810
Cov.:
32
AF XY:
0.200
AC XY:
14831
AN XY:
74270
show subpopulations
African (AFR)
AF:
0.567
AC:
23470
AN:
41402
American (AMR)
AF:
0.168
AC:
2552
AN:
15204
Ashkenazi Jewish (ASJ)
AF:
0.00577
AC:
20
AN:
3468
East Asian (EAS)
AF:
0.482
AC:
2483
AN:
5154
South Asian (SAS)
AF:
0.164
AC:
788
AN:
4814
European-Finnish (FIN)
AF:
0.00632
AC:
67
AN:
10602
Middle Eastern (MID)
AF:
0.0136
AC:
4
AN:
294
European-Non Finnish (NFE)
AF:
0.00787
AC:
535
AN:
67944
Other (OTH)
AF:
0.170
AC:
358
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
754
1507
2261
3014
3768
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
254
508
762
1016
1270
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.111
Hom.:
517
Bravo
AF:
0.229
Asia WGS
AF:
0.404
AC:
1399
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
11
DANN
Benign
0.86
PhyloP100
1.2
PromoterAI
0.0034
Neutral
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

Publications

Other links and lift over

dbSNP: rs2459394; hg19: chr15-48444748; API