GeneBe

1-40257123-G-A

Variant names:

Variant summary

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

The ENST00000567508.3(ZMPSTE24-DT):​n.872C>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 0.249 in 152,062 control chromosomes in the GnomAD database, including 4,846 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.25 ( 4846 hom., cov: 32)
Failed GnomAD Quality Control

Consequence

ZMPSTE24-DT
ENST00000567508.3 non_coding_transcript_exon

Scores

2

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 0.868

Publications

3 publications found
Variant links:
Genes affected
ZMPSTE24-DT (HGNC:55402): (ZMPSTE24 divergent transcript)

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=-0.78).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZMPSTE24-DTENST00000567508.3 linkn.872C>T non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
AF:
0.249
AC:
37898
AN:
151944
Hom.:
4847
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.253
Gnomad AMI
AF:
0.129
Gnomad AMR
AF:
0.179
Gnomad ASJ
AF:
0.217
Gnomad EAS
AF:
0.245
Gnomad SAS
AF:
0.179
Gnomad FIN
AF:
0.295
Gnomad MID
AF:
0.187
Gnomad NFE
AF:
0.265
Gnomad OTH
AF:
0.240
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:
0.249
AC:
37893
AN:
152062
Hom.:
4846
Cov.:
32
AF XY:
0.249
AC XY:
18478
AN XY:
74316
show subpopulations
African (AFR)
AF:
0.252
AC:
10449
AN:
41452
American (AMR)
AF:
0.179
AC:
2734
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
0.217
AC:
753
AN:
3468
East Asian (EAS)
AF:
0.244
AC:
1265
AN:
5180
South Asian (SAS)
AF:
0.178
AC:
860
AN:
4826
European-Finnish (FIN)
AF:
0.295
AC:
3112
AN:
10538
Middle Eastern (MID)
AF:
0.177
AC:
52
AN:
294
European-Non Finnish (NFE)
AF:
0.265
AC:
18046
AN:
67988
Other (OTH)
AF:
0.239
AC:
504
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1484
2967
4451
5934
7418
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
406
812
1218
1624
2030
<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:
0.256
Hom.:
19518
Bravo
AF:
0.241
Asia WGS
AF:
0.215
AC:
746
AN:
3478

ClinVar

Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link

Submissions by phenotype

not provided Other:1
-
ZMPSTE24 homepage - Leiden Muscular Dystrophy pages
Significance:not provided
Review Status:no classification provided
Collection Method:literature only

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
12
DANN
Benign
0.67
PhyloP100
0.87

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs926830; hg19: chr1-40722795; COSMIC: COSV65638920; API