NM_007046.4:c.2558-90G>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007046.4(EMILIN1):c.2558-90G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 1,269,510 control chromosomes in the GnomAD database, including 261,222 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 0.65 ( 33035 hom., cov: 33)
Exomes 𝑓: 0.64 ( 228187 hom. )
Consequence
EMILIN1
NM_007046.4 intron
NM_007046.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.256
Publications
14 publications found
Genes affected
EMILIN1 (HGNC:19880): (elastin microfibril interfacer 1) This gene encodes an extracellular matrix glycoprotein that is characterized by an N-terminal microfibril interface domain, a coiled-coiled alpha-helical domain, a collagenous domain and a C-terminal globular C1q domain. The encoded protein associates with elastic fibers at the interface between elastin and microfibrils and may play a role in the development of elastic tissues including large blood vessels, dermis, heart and lung. [provided by RefSeq, Sep 2009]
EMILIN1 Gene-Disease associations (from GenCC):
- neuronopathy, distal hereditary motor, autosomal dominant 10Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EMILIN1 | ENST00000380320.9 | c.2558-90G>C | intron_variant | Intron 5 of 7 | 1 | NM_007046.4 | ENSP00000369677.4 | |||
EMILIN1 | ENST00000433140.1 | c.548-90G>C | intron_variant | Intron 2 of 4 | 2 | ENSP00000411201.1 |
Frequencies
GnomAD3 genomes AF: 0.653 AC: 99328AN: 152030Hom.: 33008 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
99328
AN:
152030
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.635 AC: 710018AN: 1117362Hom.: 228187 AF XY: 0.637 AC XY: 363791AN XY: 571358 show subpopulations
GnomAD4 exome
AF:
AC:
710018
AN:
1117362
Hom.:
AF XY:
AC XY:
363791
AN XY:
571358
show subpopulations
African (AFR)
AF:
AC:
19803
AN:
26758
American (AMR)
AF:
AC:
17399
AN:
44134
Ashkenazi Jewish (ASJ)
AF:
AC:
14653
AN:
23960
East Asian (EAS)
AF:
AC:
29978
AN:
38042
South Asian (SAS)
AF:
AC:
54327
AN:
79522
European-Finnish (FIN)
AF:
AC:
34620
AN:
52738
Middle Eastern (MID)
AF:
AC:
3303
AN:
5078
European-Non Finnish (NFE)
AF:
AC:
504319
AN:
798008
Other (OTH)
AF:
AC:
31616
AN:
49122
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
14019
28038
42057
56076
70095
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
11530
23060
34590
46120
57650
<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: 0.653 AC: 99399AN: 152148Hom.: 33035 Cov.: 33 AF XY: 0.653 AC XY: 48541AN XY: 74386 show subpopulations
GnomAD4 genome
AF:
AC:
99399
AN:
152148
Hom.:
Cov.:
33
AF XY:
AC XY:
48541
AN XY:
74386
show subpopulations
African (AFR)
AF:
AC:
30817
AN:
41502
American (AMR)
AF:
AC:
7575
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
2118
AN:
3470
East Asian (EAS)
AF:
AC:
3964
AN:
5176
South Asian (SAS)
AF:
AC:
3326
AN:
4830
European-Finnish (FIN)
AF:
AC:
7014
AN:
10592
Middle Eastern (MID)
AF:
AC:
197
AN:
294
European-Non Finnish (NFE)
AF:
AC:
42608
AN:
67978
Other (OTH)
AF:
AC:
1346
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1781
3561
5342
7122
8903
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
806
1612
2418
3224
4030
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2416
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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