NM_178860.5:c.1240+10dupC
Variant names:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1
The NM_178860.5(SEZ6):c.1240+10dupC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 1,604,148 control chromosomes in the GnomAD database, including 228,868 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.61 ( 31201 hom., cov: 0)
Exomes 𝑓: 0.52 ( 197667 hom. )
Consequence
SEZ6
NM_178860.5 intron
NM_178860.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.265
Publications
6 publications found
Genes affected
SEZ6 (HGNC:15955): (seizure related 6 homolog) The protein encoded by this gene is thought to contain five cysteine-rich motifs that are similar to sushi domains, as well as two domains similar to the amino terminal half of the CUB (for complement C1r/C1s, Uegf, Bmp1) domain. Mutations in this gene have been associated with febrile seizures. [provided by RefSeq, Jul 2016]
PIPOX (HGNC:17804): (pipecolic acid and sarcosine oxidase) Enables L-pipecolate oxidase activity and sarcosine oxidase activity. Involved in L-lysine catabolic process to acetyl-CoA via L-pipecolate. Located in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.614 AC: 93263AN: 151978Hom.: 31150 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
93263
AN:
151978
Hom.:
Cov.:
0
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:
GnomAD2 exomes AF: 0.514 AC: 119382AN: 232150 AF XY: 0.512 show subpopulations
GnomAD2 exomes
AF:
AC:
119382
AN:
232150
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.516 AC: 749236AN: 1452052Hom.: 197667 Cov.: 41 AF XY: 0.515 AC XY: 371361AN XY: 721280 show subpopulations
GnomAD4 exome
AF:
AC:
749236
AN:
1452052
Hom.:
Cov.:
41
AF XY:
AC XY:
371361
AN XY:
721280
show subpopulations
African (AFR)
AF:
AC:
30670
AN:
33330
American (AMR)
AF:
AC:
19595
AN:
43366
Ashkenazi Jewish (ASJ)
AF:
AC:
13392
AN:
25900
East Asian (EAS)
AF:
AC:
13185
AN:
39434
South Asian (SAS)
AF:
AC:
44866
AN:
84294
European-Finnish (FIN)
AF:
AC:
28314
AN:
52760
Middle Eastern (MID)
AF:
AC:
3247
AN:
5704
European-Non Finnish (NFE)
AF:
AC:
564250
AN:
1107268
Other (OTH)
AF:
AC:
31717
AN:
59996
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.486
Heterozygous variant carriers
0
19007
38014
57020
76027
95034
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
16416
32832
49248
65664
82080
<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: 0.614 AC: 93361AN: 152096Hom.: 31201 Cov.: 0 AF XY: 0.611 AC XY: 45425AN XY: 74360 show subpopulations
GnomAD4 genome
AF:
AC:
93361
AN:
152096
Hom.:
Cov.:
0
AF XY:
AC XY:
45425
AN XY:
74360
show subpopulations
African (AFR)
AF:
AC:
37367
AN:
41516
American (AMR)
AF:
AC:
7948
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
1783
AN:
3470
East Asian (EAS)
AF:
AC:
1662
AN:
5166
South Asian (SAS)
AF:
AC:
2534
AN:
4820
European-Finnish (FIN)
AF:
AC:
5743
AN:
10568
Middle Eastern (MID)
AF:
AC:
168
AN:
294
European-Non Finnish (NFE)
AF:
AC:
34436
AN:
67968
Other (OTH)
AF:
AC:
1235
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1610
3219
4829
6438
8048
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
740
1480
2220
2960
3700
<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:
1574
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
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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